A Case Study in FDA Warning Letter Response and Quality System Overhaul
After an inspection revealed wide-ranging cGMP gaps, an OTC topical firm rebuilt its quality systems from the ground up.
Every year, hundreds of U.S. manufacturers receive FDA warning letters that cite different expressions of the same core deficiencies. How those problems manifest often look different, but the root story remains the same: too few people, too little structure, and too much trust that legacy processes will withstand modern scrutiny.
Earlier this year, that story became real for one topical drug manufacturer when the FDA issued a warning letter following an inspection months before.
The company, a producer of topical pain relievers, had grown steadily for decades, but its quality systems had never truly modernized. It wasn’t cutting corners so much as operating with outdated assumptions—the kind common to firms that have been “doing things this way for years” and haven’t felt the pressure to change.
When the FDA arrived for an inspection, that approach met 21 CFR Part 211 head-on.
This quick case study walks through what happened after the company engaged us for support. It’s a look at the anatomy of a successful response and quality system overhaul that was years overdue.
When the warning letter arrived
The agency’s findings will sound familiar to anyone who’s managed compliance in a lean operation:
No confirmed identity or strength testing before product release.
Unverified supplier materials accepted on the basis of unvalidated COAs.
Incomplete batch production records that didn’t fully document each manufacturing step.
A missing independent Quality Unit, leaving Quality effectively subordinate to Production.
Labeling and marketing claims that extended beyond the OTC monograph.
The FDA’s message was clear. These weren’t isolated violations as they can appear in a list of deficiencies. They reflected systemic breakdowns. An absence of documented oversight, a lack of independence, and a reactive rather than preventive approach to compliance.
The warning letter response we helped craft included a personal response from the president: “We take these findings seriously and are committed to fully addressing each cited violation and implementing sustainable CGMP compliance improvements.”
He, like virtually every company we work with in the wake of an enforcement action, meant it. But the difference between good intentions and a credible FDA response lies in structure and proof.
The situation on the ground
This firm had grown from a small regional manufacturer into a nationally distributed OTC brand. What hadn’t grown was its Quality infrastructure.
Testing and documentation had been handled locally. Suppliers were long trusted but not formally qualified.
There were no stability studies supporting the labeled shelf life.
And the same few employees often wore multiple hats across production, testing, and release.
The inspection made it all plain. Compliance could no longer depend on familiarity and institutional memory. The company needed a complete system rebuild. Not just new SOPs, but a new model for how work was controlled, verified, and documented.
Our response strategy
Our engagement began with a combination of several activities, more or less in tandem:
Developing a formal response to the warning letter.
Opening and executing CAPAs.
Authoring SOPs.
The FDA wants to see a comprehensive approach to addressing each finding in a way that would stand up under reinspection. And at the core of the project was the principle that guides all of our compliance projects: The FDA doesn’t want promises. It wants proof.
Let’s quickly break this down into each component part:
1. Structured CAPA development
Both teams worked together to open a series of CAPAs corresponding to each cited violation. Each CAPA included:
Containment measures (holding all new batches pending full laboratory testing).
Root cause analysis, identifying process-level gaps rather than blaming individuals.
Defined corrective actions, verification steps, and effectiveness checks.
The CAPAs covered testing, supplier qualification, documentation, and establishment of a Quality Unit—all under executive oversight.
2. Laboratory and supplier controls
Recognizing that its internal testing capabilities were limited, the company contracted an accredited external laboratory to perform:
Identity, purity, and stability testing for all marketed products.
DEG/EG contamination testing for glycerin and other high-risk components, per FDA guidance.
Simultaneously, we helped write and implement procedures for:
Verification and periodic revalidation of supplier Certificates of Analysis.
Risk-based supplier qualification and requalification.
Documented acceptance criteria for incoming materials and packaging components.
3. Documentation and SOP development
Our scope included over 200 hours dedicated to authoring and revising the company’s SOPs. These procedures covered laboratory operations, documentation practices, deviation management, and CAPA control. A few months later, an addendum extended the engagement to complete additional SOPs and provide follow-up implementation support as the CAPAs advanced toward closure.
4. Establishing an Independent Quality Unit
The company also acted on perhaps the most consequential of the FDA’s observations: the absence of an independent Quality Unit
Under new procedures drafted and implemented with our guidance, Quality gained full authority over batch release, investigations, and change control—ensuring all disposition decisions were made independently of production.
This structural change represented a turning point. It marked a shift from compliance-by-committee to accountability-by-design.
Results
In a matter of weeks, the company had submitted its first formal progress report to the FDA. It included:
Executed CAPAs with objective evidence of containment and completion.
Copies of laboratory contracts, test methods, and validation protocols.
A Master Validation Plan outlining a phased approach for equipment, process, and method validation.
New SOPs and batch record templates, written to align with 21 CFR Part 211 and FDA guidance.
A Quality Unit charter and updated organizational chart demonstrating independence from production.
The FDA acknowledged receipt of the report and the ongoing remediation plan.
Internally, the company had already realized some of the benefits of this work: better traceability, consistent supplier documentation, and a culture that understood why “prove it” is the language the FDA speaks best.
The company has continued working with our team through the remainder of the year to close remaining CAPAs, complete supplier requalification, and prepare for reinspection.
A few lessons for industry teams
The FDA’s observations in this case weren’t unusual—and that’s exactly why they matter. The same patterns appear in small and mid-sized OTC and contract manufacturing facilities every year in both the FDA’s letters and our own audit work. What sets successful companies apart is how they respond and what they do to avoid problems in the first place.
A few lessons here—some more obvious than others:
Treat every warning letter as a system failure, not a list of tasks to address in isolation. Each cited violation ties back to missing infrastructure: no testing because there’s no defined release process, no records because documentation isn’t standardized, no Quality authority because oversight is embedded in operations. The right response starts by mapping how those pieces connect. And they almost always do connect one way or another.
Turn CAPAs into a roadmap, not a filing requirement. Every CAPA in this project had a timeline, ownership, and an effectiveness check—and each one was traceable to a systemic fix. FDA reviewers can tell immediately whether a CAPA log is a tracking form or a management tool. The difference is evidence of progress. This is a significant oversight we often see teams make when they handle events like this (and CAPAs in general) entirely internally.
Don’t rely on “trusted” suppliers. Qualify them. This is one of the most prevalent supplier-related issues we see across the industry when we audit. The company’s unverified COAs were one of the FDA’s most serious concerns. Regulators are constantly looking for this. Implementing formal supplier qualification and requalification procedures not only closed the finding but also reduced real business risk. The takeaway: document trust as verification.
Contract labs should extend capability, not abdicate responsibility. Outsourcing testing didn’t remove the company’s obligations. We guided the creation of contracts that clearly defined ownership of data, methods, and review. Sponsors must always retain responsibility for ensuring data integrity—even when testing is external. You cannot sign your responsibilities away.
Measure completion in evidence, not declarations. The FDA doesn’t grade intent. It grades proof. Each corrective action in this engagement was closed with attachments: SOPs bearing signatures, validation summaries, executed test results, and completed training forms. “Done” meant documented, reviewed, and filed.
Need support developing or executing a Warning Letter or 483 response?
If your organization is addressing a Form 483, warning letter, or broader remediation effort, we can assist. Our network of thousands of life-science consultants —including 250 former FDA professionals—supports manufacturers in developing credible responses, executing CAPAs, writing and revising SOPs, and rebuilding quality systems that meet modern cGMP expectations.
We partner with teams at every scale to turn enforcement pressure into lasting operational strength. Drop us a line to start the conversation, and be sure to download our service explainer below.
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