The NDA Process: A Guide to FDA Submission & Approval

Last Updated on 

February 18, 2025

By 

Excedr
NDA process
Table of Contents

Other Posts About Industry Insights

Submitting a New Drug Application (NDA) to the U.S. Food and Drug Administration (FDA) is a significant milestone in drug development, marking the final step before a drug can reach patients. It represents the culmination of years of research, preclinical studies, clinical trials, and regulatory planning, all designed to demonstrate a drug’s safety, efficacy, and manufacturing quality.

A well-prepared NDA submission is essential for a smooth FDA review, helping to prevent delays and requests for additional data. Under the Food, Drug, and Cosmetic Act, all new drugs, biologics, and therapies must undergo rigorous evaluation before they can be marketed. The NDA compiles clinical trial data, pharmacology and toxicology summaries, proposed labeling, and manufacturing details to confirm that a drug’s benefits outweigh its risks.

For pharmaceutical companies and scientists, understanding the NDA process, regulatory expectations, and FDA review steps is key to securing timely approval. The NDA follows the Electronic Common Technical Document (eCTD) format, which organizes key data into five structured modules for evaluation by the Center for Drug Evaluation and Research (CDER).

This guide provides a breakdown of the NDA process:

  • NDA Submission: Key components and how to structure an application.
  • FDA Review Process: Timelines and evaluation steps.
  • Post-NDA Phase: Ongoing regulatory responsibilities after approval.

A clear understanding of the NDA process can help scientists, regulatory professionals, and clinical researchers ensure a successful review and market entry.

What Is an NDA?

No, not that kind of NDA! While non-disclosure agreements keep secrets, a New Drug Application (NDA) is all about disclosure—providing the FDA with everything it needs to approve a new drug for market.

A New Drug Application (NDA) is the formal request for FDA approval to market a new drug product in the United States. It represents the final regulatory hurdle before a drug can be legally prescribed and made available to patients.

The NDA submission compiles all necessary clinical, preclinical, pharmacology, toxicology, and manufacturing data, demonstrating that the drug is safe, effective, and consistently produced according to Good Manufacturing Practices (GMP).

At its core, an NDA serves three key purposes:

  • To confirm the drug’s safety and efficacy for its intended use.
  • To establish that the drug’s benefits outweigh its risks when used as labeled.
  • To verify that the drug can be manufactured with high quality and consistency.

Once the FDA review process is complete, the agency decides whether to approve the drug, request additional information, or reject the application.

From IND to NDA: The Regulatory Transition

Before reaching the NDA submission stage, a drug sponsor must conduct clinical trials under an Investigational New Drug (IND) application. The IND is a pre-market regulatory submission that allows pharmaceutical companies to begin testing a new drug in human subjects under FDA oversight.

The transition from IND to NDA follows key regulatory milestones:

  • IND Submission & Phase 1-2 Clinical Trials: The FDA reviews the IND before clinical trials begin. Phase 1 and 2 studies assess the drug’s safety, pharmacokinetics, and early efficacy.
  • End-of-Phase 2 Meeting with the FDA: Before moving to Phase 3 trials, sponsors meet with the FDA to discuss clinical findings, trial design, and regulatory expectations for an NDA submission.
  • Phase 3 Trials & NDA Preparation: Large-scale trials confirm the drug’s long-term safety, efficacy, and dosing, generating the final dataset for NDA submission.

The End-of-Phase 2 Meeting is a critical step in regulatory strategy, allowing the sponsor to align with FDA requirements before advancing to the final stage of drug development.

The NDA’s Legal Framework: The Federal Food, Drug, and Cosmetic Act (FDCA)

The NDA process is mandated by the Federal Food, Drug, and Cosmetic Act, which requires that all new drugs undergo rigorous FDA evaluation before being introduced to the market. Enacted in 1938, the FD&C Act was created in response to public health crises caused by unregulated drug production and strengthened federal oversight of pharmaceuticals.

Under the FD&C Act, pharmaceutical sponsors must provide scientific evidence from preclinical studies and clinical trials proving that a drug is both safe and effective. This evidence must support:

  • Intended uses as outlined in the proposed labeling.
  • Dosing recommendations for healthcare providers and patients.
  • The drug’s safety profile, including known risks and side effects.
  • Consistency in the drug’s manufacturing process to ensure high-quality production.

The FDA’s CDER is responsible for reviewing NDAs to ensure that only drugs meeting strict safety and efficacy standards are approved.

NDA vs. Other Regulatory Submissions

While an NDA is the standard approval pathway for new drugs, other regulatory submission types exist:

  • Investigational New Drug (IND) Application: Required before clinical trials begin, allowing a drug to be tested in humans. IND approval does not permit marketing—it is a research-stage submission.
  • Abbreviated New Drug Application (ANDA) – Generic Drugs: Used for generics, which must demonstrate bioequivalence to an already approved drug. ANDAs do not require extensive clinical trials.
  • Biologics License Application (BLA) – Biologics and Vaccines: Required for biological products such as monoclonal antibodies, gene therapies, and vaccines. Unlike NDAs, BLAs follow the Public Health Service Act (PHSA) rather than the FDCA and require additional purity and immunogenicity data.

Why the NDA Process Matters

The NDA review process is essential for public health and patient safety. It ensures that only well-tested, high-quality drugs reach consumers. Without it, unsafe or ineffective therapies could enter the market, putting patients at risk.

By following the FDA’s rigorous drug approval process, pharmaceutical sponsors can ensure:

  • That new drugs meet high safety and efficacy standards.
  • That healthcare providers receive clear prescribing information.
  • That patients gain access to innovative and life-saving treatments.

Avoiding regulatory hurdles doesn’t start with the NDA submission—it begins long before, in the early stages of research, testing, and regulatory planning. A well-structured pre-NDA phase ensures that all necessary data is in place, reducing the risk of delays and strengthening the foundation for a successful submission.

Laying the Groundwork: The Pre-NDA Phase

Before submitting an NDA, pharmaceutical sponsors must complete extensive preclinical and clinical research to generate the scientific evidence required for approval. The pre-NDA phase consists of:

  • Preclinical Research & IND Submission: Conducting toxicology and pharmacokinetics (PK) studies in animal models to assess safety. Submitting an Investigational New Drug (IND) application to the FDA to initiate human trials.
  • Clinical Trials (Phases 1-3): Phase 1 involves evaluating basic safety, tolerability, and PK in a small number of subjects. Phase 2 involves assessing efficacy, side effects, and optimal dosing in the target patient population. And Phase 3 includes large-scale randomized controlled trials (RCTs) confirm long-term efficacy and safety.
  • Pre-NDA Meeting with the FDA: This meeting provides an opportunity to clarify regulatory requirements, confirm labeling expectations, and address any gaps in clinical data before submission.
  • Manufacturing Readiness & CMC Compliance: Demonstrating batch consistency, Good Manufacturing Practices (GMP) compliance, and drug stability to ensure reliable production.

A well-executed pre-NDA phase helps sponsors avoid regulatory delays, minimize the risk of a Complete Response Letter (CRL), and ensure all necessary data is in place before submission. With this groundwork complete, the focus shifts to structuring a clear, well-organized NDA submission that meets FDA requirements and maximizes the chances of first-cycle approval.

NDA Submission: Key Components

The NDA submission is the culmination of years of drug development, preclinical studies, and clinical trials. It serves as the formal request for FDA approval, providing the data and documentation necessary to demonstrate that a drug product is safe, effective, and can be consistently manufactured to high standards.

A well-structured NDA is essential for a smooth FDA review process and increases the likelihood of first-cycle approval without delays. It must be structured according to the Common Technical Document (CTD) format, which organizes regulatory submissions into five key modules. This format ensures global harmonization and makes it easier for FDA reviewers to analyze the data efficiently.

Module 1: Administrative & Regulatory Information

This section includes all essential forms, regulatory documents, and compliance information:

  • Cover Letter: A summary of the NDA submission, highlighting key data and the drug’s intended use.
  • Form FDA 356h: The official form requesting FDA approval for a prescription drug product.
  • Patent & Exclusivity Information: Documentation on intellectual property protections and regulatory exclusivity claims.
  • Prescription Drug User Fee Act (PDUFA) Fee Documentation: Proof of required user fee payments that support the FDA drug approval process.

Module 2: Summaries of Safety, Efficacy & Clinical Studies

This module provides high-level summaries of clinical trial data, pharmacology, and toxicology to give FDA reviewers a concise overview of the submission.

  • Integrated Summary of Safety (ISS): A combined analysis of safety findings from clinical trials.
  • Integrated Summary of Efficacy (ISE): A review of the drug’s effectiveness across all studies.
  • Clinical Pharmacology & Pharmacokinetics Summary: An overview of absorption, metabolism, distribution, and excretion (ADME).
  • Toxicology Summary: Key preclinical toxicology findings from animal studies.

Module 3: Chemistry, Manufacturing & Controls (CMC)

The CMC section is critical in proving that the drug can be consistently manufactured with high quality and reliability.

  • Drug Substance & Drug Product Information: The chemical composition and formulation of the drug.
  • Manufacturing Processes & GMP Compliance: Documentation proving that facilities meet FDA standards for Good Manufacturing Practices (GMP).
  • Stability & Shelf-Life Data: Evidence supporting the drug’s long-term storage conditions and expiration date.

Module 4: Nonclinical Study Reports

This module contains detailed reports from preclinical (animal) studies, which provide early safety and pharmacology data.

  • Toxicology Studies: Findings on short- and long-term toxicity, carcinogenicity, and reproductive safety.
  • Pharmacokinetics & Pharmacodynamics Data: Studies on how the drug interacts with biological systems.

Module 5: Clinical Study Reports

This is the most extensive part of the NDA and contains raw clinical trial data, study designs, and statistical analyses.

  • Phase 1, 2, and 3 Clinical Trial Data: Comprehensive reports on safety, efficacy, and dosing.
  • Statistical Analysis Reports: In-depth evaluation of data reliability and significance.
  • Risk-Benefit Analysis: Justification that the benefits outweigh potential side effects.

The NDA Submission Process, Summarized

A well-prepared NDA submission is the final step before FDA approval and serves as a comprehensive record of a drug's safety, efficacy, and manufacturing quality. By following the Common Technical Document (CTD) format, sponsors present critical clinical trial data, pharmacology summaries, and regulatory documentation in a structured manner that facilitates efficient FDA review.

Each module of the NDA submission plays a crucial role:

  • Administrative & Regulatory Information (Module 1) ensures all required forms and compliance documents are in place.
  • Summaries of Safety, Efficacy & Clinical Studies (Module 2) provide a high-level overview of the drug’s performance.
  • Chemistry, Manufacturing & Controls (Module 3) demonstrates GMP compliance and drug stability for consistent production.
  • Nonclinical Study Reports (Module 4) contain toxicology and pharmacokinetics data from preclinical studies.
  • Clinical Study Reports (Module 5) present detailed Phase 1-3 trial data, statistical analyses, and risk-benefit assessments.

A well-organized NDA increases the likelihood of first-cycle approval, reducing the risk of delays or additional FDA requests that could slow the approval process.

With the NDA submitted, the FDA begins its formal review, assessing the application’s completeness, scientific rigor, and compliance with regulatory standards. Navigating this process successfully requires an understanding of key review stages, timelines, and potential challenges.

How to Submit an NDA

The FDA requires most NDA submissions to follow the Electronic Common Technical Document (eCTD) format, a structured digital submission system designed to improve efficiency, accuracy, and communication between sponsors and regulatory reviewers.

Using the eCTD format offers several advantages:

  • Ensures uniform data formatting for easier FDA review.
  • Reduces submission errors and missing documentation by following a standardized framework.
  • Allows seamless communication between the sponsor and FDA reviewers, enabling structured feedback and responses.

Key Steps in the NDA Submission Process

  1. Assemble the NDA in eCTD Format: Sponsors must structure the five modules of the eCTD into an electronic submission package that meets FDA validation criteria.
  2. Conduct a Pre-Submission Validation Check: Before submitting, sponsors should run an electronic validation to detect missing files, formatting errors, or compliance issues that could delay processing.
  3. Submit Through the FDA Electronic Submissions Gateway (ESG): The FDA ESG is the agency’s secure portal for accepting eCTD submissions. Sponsors must first register and obtain an ESG account before uploading their NDA.
  4. Confirm Receipt & Track Review Status: Once submitted, the FDA provides an Acknowledgment of Receipt, confirming that the submission was successfully received and entered into the review pipeline.

For detailed FDA submission guidelines, sponsors can start here.

FDA Review Process: What Happens After Submission

Once an NDA is submitted, the FDA has 60 days to determine whether the application is complete and ready for formal review. If accepted, the NDA moves into the FDA review process, which typically takes 6 to 10 months, depending on whether the drug qualifies for Priority Review.

The review process involves multiple steps, including an initial filing review, scientific and regulatory evaluations, advisory committee meetings (if required), and a final decision on approval. Understanding the timeline and key steps in the drug review process helps pharmaceutical companies and regulatory teams anticipate challenges and prepare responses efficiently.

FDA Filing Review (First 60 Days)

Once the NDA submission is received, the FDA has 60 days to conduct an initial filing review to determine whether the application is complete and ready for full evaluation.

  • If the FDA determines that the submission is incomplete, it issues a Refuse-to-File (RTF) letter, requiring the sponsor to provide additional information before review can begin.
  • If the FDA accepts the NDA, the application is assigned a review designation (Standard Review or Priority Review) and moves forward in the approval process.

Here are the review designations you can receive:

  • Standard Review: The typical NDA review timeline is 10 months.
  • Priority Review: If the drug product addresses an unmet medical need or offers significant advantages over existing therapies, the FDA assigns a Priority Review designation, shortening the review process to 6 months.

The Prescription Drug User Fee Act (PDUFA) timelines ensure that the FDA meets specific deadlines for evaluating NDAs.

Scientific & Regulatory Review (6 to 10 Months)

Once an NDA passes the filing review, the FDA initiates an in-depth scientific and regulatory evaluation to determine whether the drug product meets the necessary standards for safety, efficacy, and manufacturing quality. This phase involves a comprehensive review of clinical, preclinical, and manufacturing data, ensuring compliance with FDA guidance documents, federal food regulations, and international standards.

To conduct a thorough evaluation, the FDA assembles a multidisciplinary review team composed of experts in clinical data, pharmacology, toxicology, manufacturing, and statistical analysis. Let’s break down the role each expert plays in the review process.

FDA Review Teams & Areas of Focus

The Center for Drug Evaluation and Research (CDER) assembles a multidisciplinary review team with expertise in clinical, nonclinical, statistical, and manufacturing sciences. Each expert evaluates specific components of the submission:

  • Medical Officers: Assess clinical trial data to determine the drug’s safety profile, efficacy, and potential side effects in the intended patient population.
  • Pharmacologists & Toxicologists: Review preclinical research, pharmacokinetics (PK), pharmacodynamics (PD), and toxicity data from animal studies to identify any safety concerns.
  • Chemistry, Manufacturing, and Controls (CMC) Reviewers: Evaluate drug formulation, stability, and manufacturing processes to ensure adherence to Good Manufacturing Practices (GMP) and consistent product quality.
  • Statisticians: Perform independent statistical analyses to confirm the significance and reliability of clinical trial results.
  • Labeling Experts: Review the proposed labeling, package insert, and dosing recommendations to ensure clear, accurate information for healthcare providers and patients.

By breaking down the review like this, the can ensure the process is structured and methodical and make sure that the drug’s benefits outweigh risks and that all regulatory requirements are met before approval.

If the FDA determines that additional expertise is needed to evaluate a drug’s safety, efficacy, or public health impact, it may convene an Advisory Committee Meeting. This panel of independent experts provides recommendations that can influence the final approval decision.

Advisory Committee Meeting (If Required)

For high-profile or complex drug approvals, the FDA may convene an Advisory Committee Meeting to seek independent expert opinions on safety, efficacy, and public health impact. These committees consist of scientists, clinicians, and regulatory experts who:

  • Review NDA data, clinical study results, and identified safety concerns.
  • Evaluate whether the drug’s benefits outweigh its risks.
  • Vote on a recommendation for approval, rejection, or additional study requirements.

While the FDA is not required to follow the committee’s recommendation, these meetings often heavily influence the final decision.

Before granting final approval, the FDA conducts pre-approval inspections and works with the sponsor to finalize the drug’s labeling. These steps ensure that the drug can be manufactured consistently and that prescribing information accurately reflects its safe and effective use.

Pre-Approval Inspections & Labeling Finalization

Before FDA approval, the agency conducts pre-approval inspections (PAI) and labeling finalization to ensure the drug product is safe, manufacturable, and appropriately labeled for use.

  • Pre-Approval Inspections (PAI): FDA inspectors visit manufacturing facilities to evaluate:
    • Compliance with Good Manufacturing Practices (GMP).
    • The reliability and quality control processes in place to ensure consistent drug production.
    • Any potential risks in drug storage, stability, and packaging.
  • Labeling Negotiations: The FDA works with the sponsor to finalize the proposed labeling, including:
    • Indications, dosing instructions, and administration guidelines.
    • Contraindications, safety warnings, and potential adverse reactions.
    • Packaging and prescribing information for healthcare providers.

If manufacturing issues arise or if labeling requires modifications, the approval timeline may be delayed until all outstanding concerns are addressed.

FDA Approval or Rejection

At the end of the review process, the FDA issues one of two possible decisions:

  • Approval Letter: If the NDA review process confirms that the drug is safe, effective, and meets regulatory requirements, the FDA grants market approval. The sponsor can begin commercial distribution with the approved labeling and prescribing information.
  • Complete Response Letter (CRL): If the FDA identifies deficiencies in clinical data, manufacturing, or safety concerns, it issues a Complete Response Letter (CRL) outlining required additional information before approval can be reconsidered. Sponsors must address the deficiencies and submit a resubmission or conduct further studies before obtaining FDA approval.

Receiving FDA approval for a new drug application (NDA) is a major milestone, but regulatory responsibilities do not end once a drug product reaches the market. The post-NDA phase invovles ensuring long-term safety, monitoring real-world effectiveness, and maintaining compliance with FDA regulations.

Post-NDA Phase: Ongoing Regulatory Responsibilities After Approval

Even after approval, the FDA’s Center for Drug Evaluation and Research (CDER) continues to assess the drug’s safety profile, manufacturing quality, and potential risks. Pharmaceutical companies must remain actively engaged in post-marketing surveillance, adverse event reporting, and regulatory compliance to prevent safety concerns from leading to labeling updates, market restrictions, or even withdrawal of the drug from the market.

Let’s break down the key components of this phase.

Post-Marketing Surveillance & Phase 4 Clinical Trials

Once a drug product reaches the market, it is used by a much larger and more diverse patient population than those studied in clinical trials. This increased exposure may reveal previously undetected side effects or rare adverse reactions that were not observed during the FDA review process.

  • Post-Marketing Surveillance (PMS): The FDA monitors real-world drug use through spontaneous adverse event reports, healthcare provider feedback, and large-scale observational studies.
  • Phase 4 Clinical Trials: Some drugs require post-marketing (Phase 4) studies to gather additional data on long-term safety, efficacy, or new indications.
  • FDA’s Sentinel Initiative: A national system used to track real-world adverse events, drug interactions, and emerging safety concerns.

If significant safety issues arise, the FDA may require further studies, updates to the prescribing information, or additional risk management measures.

Adverse Event Reporting & Pharmacovigilance

Pharmaceutical companies must maintain a robust pharmacovigilance program to track and report adverse events, serious side effects, and safety concerns.

  • Mandatory Adverse Event Reporting: Sponsors must submit Periodic Adverse Drug Experience Reports (PADERs) and Periodic Benefit-Risk Evaluation Reports (PBRERs) to summarize ongoing safety data.
  • Healthcare Provider & Patient Reports: Physicians, pharmacists, and consumers can report side effects or adverse reactions directly to the FDA’s MedWatch system.
  • Safety Signal Analysis: If patterns of unexpected toxicity, drug interactions, or serious risks emerge, the FDA may conduct additional investigations.

Proactive pharmacovigilance helps ensure that potential safety concerns are identified and addressed before they become widespread issues.

Labeling Updates & Risk Management Strategies (REMS)

The proposed labeling included in an NDA may require updates post-approval based on new safety findings, drug interactions, or clinical trial data.

  • Labeling Updates: If new risks, precautions, or dosage modifications are identified, the FDA may require changes to the drug’s package insert, warnings, or contraindications.
  • Risk Evaluation and Mitigation Strategies (REMS): For drugs with serious safety concerns, the FDA mandates REMS programs to ensure they are used safely. These strategies may include:
    • Prescriber training requirements
    • Restricted distribution programs
    • Enhanced patient monitoring protocols

Regulatory affairs teams must work closely with the FDA to ensure that labeling changes and safety updates are implemented correctly and communicated effectively to healthcare providers and patients.

Continued Manufacturing Compliance & Inspections

Good Manufacturing Practices (GMP) compliance does not end with FDA approval. The FDA continues to inspect manufacturing facilities to ensure that the drug is produced consistently and meets quality standards.

  • Routine Post-Approval Inspections: The FDA inspects manufacturing sites to confirm adherence to GMP regulations.
  • Supply Chain Monitoring: Sponsors must ensure active pharmaceutical ingredients (API) and excipients meet quality and purity standards.
  • Batch Testing & Recalls: If manufacturing issues arise, the FDA can mandate product recalls or require corrective actions.

Failure to maintain GMP compliance can result in warning letters, fines, or product withdrawal from the market.

Regulatory Responsibilities After Approval

Once an NDA is approved, the sponsor must maintain ongoing regulatory compliance with the FDA’s post-marketing requirements. This includes:

  • Regular safety reporting (PADERs, PBRERs, and FAERS submissions).
  • Updating proposed labeling to reflect new safety data or clinical findings.
  • Ensuring continued compliance with GMP and manufacturing regulations.
  • Monitoring global regulatory requirements if the drug is approved in multiple markets.
  • Responding to FDA safety alerts or additional requests for data.

Maintaining strong regulatory oversight and pharmacovigilance ensures that the drug remains safe, effective, and compliant with FDA guidelines.

The Post-NDA Phase, Summarized

FDA approval is not the final step in a drug’s regulatory journey. The post-NDA phase is crucial for ensuring long-term safety, effectiveness, and compliance as the drug reaches a larger, real-world patient population. Pharmaceutical companies must remain actively engaged in post-marketing surveillance, pharmacovigilance, and manufacturing oversight to detect and address any emerging risks.

Key components of the post-NDA phase include:

  • Post-Marketing Surveillance & Phase 4 Clinical Trials to monitor real-world safety and identify potential new risks.
  • Adverse Event Reporting & Pharmacovigilance to track and analyze adverse reactions reported by healthcare providers and patients.
  • Labeling Updates & Risk Management Strategies (REMS) to ensure prescribing information reflects new safety data and mitigate potential risks.
  • Continued Manufacturing Compliance & Inspections to maintain Good Manufacturing Practices (GMP) and prevent production-related issues.
  • Ongoing Regulatory Responsibilities to ensure adherence to FDA’s safety monitoring and reporting requirements.

A proactive approach to post-approval compliance helps prevent regulatory setbacks such as safety warnings, recalls, or product withdrawals. By consistently monitoring safety and manufacturing standards, sponsors can maintain market access while ensuring patient safety.

Avoiding these hurdles starts long before approval. Even with careful planning, the NDA process is complex, and sponsors often face challenges that delay approval or require additional regulatory submissions. The next section explores common pitfalls—such as insufficient clinical data, manufacturing compliance failures, or inadequate pharmacovigilance plans—and how to avoid them.

Wrapping Up: The Importance of a Strong NDA Submission

The NDA submission and approval process represents one of the most critical milestones in drug development, requiring a strategic, data-driven approach to secure regulatory approval and long-term market success. From the initial IND application and preclinical research to the FDA review process and post-marketing commitments, each phase plays a vital role in demonstrating a drug’s safety, efficacy, and quality.

Sponsors who prioritize regulatory compliance, rigorous clinical and statistical analysis, and proactive engagement with the FDA can reduce delays, streamline approval, and ensure patient access to safe and effective therapies. Beyond approval, ongoing pharmacovigilance, risk management, and GMP adherence remain essential in maintaining market authorization and upholding public health standards.

By adopting a well-structured regulatory strategy, engaging with the FDA early, and adhering to best practices in submission preparation, sponsors can increase their chances of first-cycle approval and bring safe, effective therapies to market more efficiently.

Other Posts About Industry Insights

Resources for founders, scientists, and the life sciences community.