You've done the science. Your preclinical data is solid. Your manufacturing process is ready. You're preparing your Investigational New Drug (IND) application and you're on track for submission in Q1.
Then, 2 weeks before submission, your QA team finds it: a critical SOP that wasn't properly approved. Or a training record that's incomplete. Or a document version that's not properly tracked.
These seem like paperwork problems. But to the FDA, they're evidence that your quality system isn't robust. And delays to IND submission are expensive—they can cost millions in delayed timelines and lost momentum.
Here are the five most common document control mistakes we see, and how to avoid them:
Mistake #1: Incomplete Version Control
The Problem: Your SOP exists in 5 versions across email, shared drives, and desktop computers. Version 1 is outdated. Version 2 was supposed to replace it but everyone forgot. Nobody knows which is the "official" version.
What the FDA sees: A company that doesn't control its quality documents. This raises red flags about data integrity throughout your operation.
How to fix it: Implement a single source of truth for all documents. Every SOP should have a clear version number, effective date, and retirement date. Old versions should be archived (never deleted). Your team should know exactly which version is current.
Mistake #2: Missing or Incomplete Approvals
The Problem: Your SOP was drafted by Research, but nobody bothered getting Quality Assurance approval. Or it was approved by one person, but your SOP says it needs two signatures. Or it was approved but not by the people specified in your organizational chart.
What the FDA sees: Processes that aren't properly controlled. If your SOPs can be implemented without proper oversight, what else is skipping necessary approvals?
How to fix it: Define your approval workflows clearly. For each SOP, specify who must review and approve (by title and department). Use your QMS to enforce these workflows. Don't allow a document to be marked "approved" until all required signatures are in place.
Mistake #3: No Audit Trail for Changes
The Problem: You have a version history of your documents, but nobody can see who made each change or when. You just know that Version 4 is different from Version 3, but not how or why.
What the FDA sees: Incomplete documentation that fails to meet 21 CFR Part 11 requirements for audit trails. This is a critical compliance gap.
How to fix it: Your QMS should maintain a complete audit trail. Every edit should be logged with: who made it, when, and optionally, why. This is a technical requirement of 21 CFR Part 11. If your QMS doesn't provide this automatically, it's not suitable for pharma.
Mistake #4: Missing Training Records
The Problem: You have SOPs for every critical process, but you can't document that everyone on your team has been trained on them. Or training records exist, but they're scattered across different systems.
What the FDA sees: Lack of evidence that your team understands your quality procedures. This is particularly problematic for roles directly involved in product manufacturing or testing.
How to fix it: Centralize all training records in your QMS. For each critical SOP, require completion of associated training. Track training dates and renewal dates. During your QMS go-live, backfill training records for existing employees to show they've been trained on current procedures.
Mistake #5: Inconsistent Document Naming and Organization
The Problem: Your SOPs are named randomly: "Manufacturing_Process_V3_Final_REAL.docx" and "SOP - Cleaning Equipment.doc" and "Sterilization Procedure (JM edits).xls". They're scattered across folders with inconsistent naming schemes. Finding a specific document takes 20 minutes.
What the FDA sees: Disorganization that suggests quality isn't being taken seriously. If you can't even organize your documents, what other quality shortcuts are you taking?
How to fix it: Establish a clear document numbering scheme and organization hierarchy. Example: "QOP-MFG-001-Manufacturing Process" or "SOP-LAB-002-Sample Analysis". Organize by department and function. Use a QMS that enforces consistent categorization. This takes time to implement initially, but saves enormous amounts of time during audits and inspections.
The Bottom Line
Document control isn't bureaucratic busy work. It's the foundation of your quality system. When your documentation is organized, controlled, and auditable, it gives the FDA (and your investors, and your team) confidence that you're operating a serious quality operation.
More importantly, good document control prevents mistakes in your actual operations. When your SOP for manufacturing is clearly written, properly approved, and regularly trained on—people follow it correctly. That's what translates to safer products and smoother regulatory approvals.
Before you submit that IND, do a document control audit. Can you answer these questions?
- Is every SOP in a single system?
- Does every SOP have the required approvals?
- Can you show the complete audit trail for every document?
- Is everyone trained on the SOPs they need?
- Could the FDA easily find and review any specific document?
If you answered "no" to any of these, you have work to do. But that work is worth it.
Is document control bogging down your startup? See how SwiftDocs streamlines document management or start your free trial to get your documentation organized before IND submission.