This informal CPD article ‘Cleanroom Layout Mistakes That Keep Showing Up in Inspection Reports’, was provided by Pharmalliance Consulting, who offer specialist support to pharmaceutical companies to maintain and increase quality compliance levels.
A cleanroom isn’t just a controlled environment; it’s a designed experience. Every door, airlock, bench, and corridor should guide people and materials through a logical, risk- reducing flow. When it doesn’t, contamination risk creeps in, and so do regulatory citations. Inspectors have been clear: poor facility layout is not just inefficient. It’s a GMP failure.
Where Layouts Go Wrong
In recent inspections across the EU and FDA-regulated sites, common layout failures include:
- Shared pathways for personnel and materials, with no segregation between incoming raw materials and processed goods.
- No clear separation between “dirty” and “clean” gowning areas.
- Multi-use areas without dedicated space for quarantined, released, and rejected materials.
- Airlocks used improperly, or worse, bypassed entirely.
These aren’t theoretical risks. They’re basic GMP expectations.
Annex 1’s Message Is Clear
The revised EU Annex 1 places strong emphasis on flow design and contamination control. Section 4.1 requires that facilities ensure “logical, effective, and segregated flows of personnel, equipment, and materials.”
It’s not enough to draw a flowchart for the auditor. They expect to see that layout
decisions are based on:
- Quality risk management principles.
- A document Contamination Control Strategy (CCS).
- Actual practices that match the intended design.
Warehouse Woes
It’s not just cleanrooms. Warehouse and material storage areas are drawing increased
scrutiny too. In multiple EU and FDA inspections, firms were cited for:
- No segregation of quarantined/released product, leading to mix-up risk.
- Unprotected loading bays, allowing water or pest ingress during deliveries.
- Storing active ingredients and excipients in the same space with no barriers or risk assessment.
These are layout decisions as much as they are procedural ones. A well-designed
warehouse doesn’t rely on SOPs to prevent mix-ups, it physically prevents them.
Unidirectional Flow Is Still a Weak Spot
Despite being a well-known principle, unidirectional flow is still a major inspection finding.Inspectors continue to note cases where personnel double back through clean areas, or where materials cross paths in uncontrolled ways. In one example, a site received a critical observation after auditors observed carts with incoming sterile components being wheeled through areas designated for waste removal. Even when a facility layout appears sound on paper, inspectors want to see how the space is actually used during normal operations.
Designing for Compliance, Not Convenience
It’s common to see facilities that were originally built for one type of product and then repurposed over time. While adaptation is sometimes necessary, inspectors expect that design changes are driven by contamination control, not convenience. A number of recent citations have pointed to ad hoc changes that bypassed formal risk assessment. Adding a new piece of equipment or rerouting a hallway may seem minor, but if it compromises separation or air handling, it becomes a compliance issue.
Operator Behaviour Reflects Layout Quality
During inspections, how people use the space says just as much as the drawings do. Inspectors have called out situations where operators take unnecessary detours, remove PPE in the wrong zones, or shortcut transfer procedures. These behaviours often stem from poor layout planning. If a cleanroom is designed with awkward flows or impractical entry sequences, people will find workarounds. Rather than blaming the operator, inspectors often look at whether the facility design made correct behaviour intuitive or difficult.
Conclusion
Layout is one of the most fundamental ways to design quality into a facility. Done poorly, it creates ongoing workarounds, training gaps, and regulatory headaches. Done well, it becomes invisible, because it supports good practice without resistance. Inspectors aren’t just following maps. They’re looking at how people move, how materials are transferred, and how design supports (or undermines) control. If the layout doesn’t tell a clear story, the inspection report will.
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References
U.S. Food and Drug Administration, 2023. Warning Letters Database, United States of America.
The European Commission, 2022. EU Annex 1, Brussels, Belgium.
European Medicines Agency, 2013. EudraGMP Database, Amsterdam, The Netherlands.
