CTD Module 3 explained with the full ICH M4Q table of contents
CTD Module 3 is the Quality part of the dossier. ICH M4Q table of contents for 3.2.S and 3.2.P, what goes where, and what the R2 draft would change.
CTD Module 3 quality section and table of contents
CTD Module 3 is the Quality part of the Common Technical Document: the full chemistry, manufacturing and controls (CMC) data for the drug substance and the drug product. Its structure is set by the ICH M4Q(R1) guideline: 3.1 Table of Contents, 3.2 Body of Data (3.2.S drug substance, 3.2.P drug product, 3.2.A appendices, 3.2.R regional information) and 3.3 Literature References.
Where Module 3 sits in the CTD
The CTD has five modules. Module 1 holds regional administrative and prescribing information, and the ICH M4(R4) guideline shows it outside the harmonised CTD. Modules 2 to 5 are intended to be common to all regions: Module 2 holds the summaries, Module 3 is Quality, Module 4 holds the nonclinical study reports and Module 5 the clinical study reports.
M4Q places quality information. It does not set how much data you need. The type and extent of supporting data "may depend upon regional guidance" (M4Q(R1)), so content expectations come from regional rules and the ICH quality guidelines.
The ICH M4Q guideline and its versions
M4Q reached Step 4 on 8 November 2000. The R1 revision, dated 12 September 2002, changed numbering and section headers, and ICH lists it at Step 5 on its CTD page. The companion M4Q Q&A (R1) is dated 17 July 2003.
The FDA publishes "Guidance for Industry M4Q: The CTD: Quality", final in August 2001 (PDF), with a location Q&A from June 2004. In the EU, EMA made M4Q (CPMP/ICH/2887/99) effective on 1 July 2003 and the Q&A on 1 August 2003.
CTD Module 3 table of contents
The M4Q(R1) table of contents identifies 3.2.S by "(name, manufacturer)" and 3.2.P by "(name, dosage form)".
3.2.S Drug substance
| Section | Subsections |
|---|---|
| S.1 General Information | S.1.1 Nomenclature; S.1.2 Structure; S.1.3 General Properties |
| S.2 Manufacture | S.2.1 Manufacturer(s); S.2.2 Description of Manufacturing Process and Process Controls; S.2.3 Control of Materials; S.2.4 Controls of Critical Steps and Intermediates; S.2.5 Process Validation and/or Evaluation; S.2.6 Manufacturing Process Development |
| S.3 Characterisation | S.3.1 Elucidation of Structure and other Characteristics; S.3.2 Impurities |
| S.4 Control of Drug Substance | S.4.1 Specification; S.4.2 Analytical Procedures; S.4.3 Validation of Analytical Procedures; S.4.4 Batch Analyses; S.4.5 Justification of Specification |
| S.5 Reference Standards or Materials | |
| S.6 Container Closure System | |
| S.7 Stability | S.7.1 Stability Summary and Conclusions; S.7.2 Post-approval Stability Protocol and Stability Commitment; S.7.3 Stability Data |
3.2.P Drug product
| Section | Subsections |
|---|---|
| P.1 Description and Composition of the Drug Product | |
| P.2 Pharmaceutical Development | P.2.1 Components of the Drug Product (P.2.1.1 Drug Substance; P.2.1.2 Excipients); P.2.2 Drug Product (P.2.2.1 Formulation Development; P.2.2.2 Overages; P.2.2.3 Physicochemical and Biological Properties); P.2.3 Manufacturing Process Development; P.2.4 Container Closure System; P.2.5 Microbiological Attributes; P.2.6 Compatibility |
| P.3 Manufacture | P.3.1 Manufacturer(s); P.3.2 Batch Formula; P.3.3 Description of Manufacturing Process and Process Controls; P.3.4 Controls of Critical Steps and Intermediates; P.3.5 Process Validation and/or Evaluation |
| P.4 Control of Excipients | P.4.1 Specifications; P.4.2 Analytical Procedures; P.4.3 Validation of Analytical Procedures; P.4.4 Justification of Specifications; P.4.5 Excipients of Human or Animal Origin; P.4.6 Novel Excipients |
| P.5 Control of Drug Product | P.5.1 Specification(s); P.5.2 Analytical Procedures; P.5.3 Validation of Analytical Procedures; P.5.4 Batch Analyses; P.5.5 Characterisation of Impurities; P.5.6 Justification of Specification(s) |
| P.6 Reference Standards or Materials | |
| P.7 Container Closure System | |
| P.8 Stability | P.8.1 Stability Summary and Conclusion; P.8.2 Post-approval Stability Protocol and Stability Commitment; P.8.3 Stability Data |
3.2.A, 3.2.R and 3.3
- 3.2.A Appendices: A.1 Facilities and Equipment; A.2 Adventitious Agents Safety Evaluation; A.3 Excipients.
- 3.2.R Regional Information.
- 3.3 Literature References: key literature referenced, if applicable.
Watch two titles that old templates get wrong. 3.2.A.3 is "Excipients", not "Novel Excipients". The Q&A explains the change: the appendix also covers non-compendial excipients that are not novel. And P.8.1 ends in "Conclusion" while S.7.1 ends in "Conclusions".
What goes in 3.2.S and 3.2.P
S.1.1 gives names such as the INN, USAN, JAN or BAN, and the CAS number. S.2.3 covers raw and starting materials, solvents, reagents and catalysts, where each is used and how each is controlled. S.2.5 shows the process, including reprocessing, is suitable and justifies critical process controls, such as cell culture and purification steps (M4Q(R1)).
P.1 lists every component with its amount per unit (overages included), its function and its quality standard. P.2 shows that the dosage form, formulation, process, container closure, microbiological attributes and usage instructions suit the purpose, and it identifies the critical parameters. It also discusses differences between the pivotal clinical batch process and the commercial process. P.3.2 gives the amounts per batch. Any proposal to reprocess is justified in P.3.3, and P.3.5 covers validation of critical steps such as sterilisation, aseptic processing or filling. P.8.1 states storage conditions, shelf-life and in-use shelf-life (M4Q(R1)).
Cross-refer to drug substance data where the guideline allows it. M4Q(R1) limits P.5.5 to impurities not already discussed in S.3.2, and P.6 to reference standards not already in S.5.
For biotech products, A.1 holds facility diagrams, shared-area information, product-contact equipment and cross-contamination controls. A.2 covers TSE agents, viral safety of animal or human-origin materials and cell banks, and viral clearance studies. Per the Q&A, routine controls for bacteria, mycoplasma and fungi go in 3.2.S or 3.2.P, while TSE agents and prions stay in 3.2.A.2.
3.2.R isn't harmonised. Each region sets its document titles and order. M4Q(R1) lists Executed Batch Records, a Method Validation Package and Comparability Protocols as US-only items. Its EU-only items are a Process Validation Scheme for the Drug Product (planned studies, if validation is not finished) and Medical Device information. In the EU, a TSE certificate of suitability goes in 3.2.R, per EMA's CEP Q&A of 28 January 2026.
CTD Module 3 example structures
The M4Q Q&A and the granularity annex of M4(R4) cover repeated sections in a pharmaceutical dossier:
- Two drug substances: a full 3.2.S for each.
- One substance from two sites with different processes: separate sections are allowed, and recommended if the specifications differ. Label them in parentheses, for example "Drug Substance (Name, Manufacturer A)".
- 100 mg tablets in a PVC blister and a PE bottle: one 3.2.P with one set of P.1 to P.8, with the container data split by type within P.7 and P.8.
- A product with a reconstitution diluent: two sections, "3.2.P (Drug Product)" and "3.2.P (Diluent)".
- A novel or non-compendial excipient with substantial data: a complete 3.2.A.3 per excipient, in the 3.2.S format.
The annex advises against a "manufacturer" label when you don't need multiple 3.2.S or 3.2.P sections.
The M4Q Q&A shows how polymorphism data spans Module 3. The form used goes in S.1.3, and S.2.2 states the form synthesised. S.3.1 holds the screening studies and how many forms were found. The limit sits in S.4.1 with its justification in S.4.5, the effect on the product in P.2.1.1 and P.2.2.3, and any product control in P.5.1 and P.5.6.
Release and shelf-life specifications both go in P.5.1. Extractables and leachables are discussed in P.2.4. Leachables, when warranted, also go in P.5.1 and P.5.5, and shelf-life leachables data go in P.8.3. Bioanalytical methods go in Module 4 (4.2.2.1) or Module 5 (5.3.1.4), not in Module 3.
Module 2.3, the Quality Overall Summary
The QOS in Module 2.3 follows the scope and outline of Module 3. It "should not include information, data or justification that was not already included in Module 3 or in other parts of the CTD" (M4Q(R1)). It normally should not exceed 40 pages of text, excluding tables and figures, or 80 pages for biotech products and complex processes (M4Q(R1)).
What the M4Q(R2) draft would change
ICH endorsed the M4Q(R2) draft for consultation on 14 May 2025 (ICH CTD page). The draft would rename Module 2.3 the "Quality Overview" and make it the basis for assessment. Module 3 would become a supporting repository organised by component, such as substances, products, excipients and impurities (EMA Step 2b draft). ICH's mapping document says the draft would drop the R1 Quality Overall Summary, replaced by 2.3.3 and 2.3.4. The FDA published its draft guidance in January 2026.
The ICH work plan aims for Step 4 adoption in June 2027. That date is a plan, not an adoption. M4Q(R1) remains the current guideline.
Where the CTD format is required
The US and the EU require the CTD structure, submitted as eCTD: the FDA for NDAs, ANDAs and BLAs, and the EMA for marketing authorisation submissions. India's 2010 CDSCO guidance says CDSCO decided to adopt the CTD format for new drug import, manufacture and marketing approval.
RegAffairs AI has a cited answer on what goes where in CTD Module 3 that links each point to the M4Q text.