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Cleanroom design challenges across industries
How to get it right from pharma to semiconductors
Every cleanroom tells a story. Sometimes it’s about precision and performance. Other times (unfortunately) it’s about a project that looked perfect on paper but failed in reality. At Jansen Cleanrooms & Labs, we’ve spent more than 30 years designing and building controlled environments for pharma, biotech, microelectronics, and healthcare. Here’s what we’ve learned about the challenges that define each, and how to design for success from the start.
The foundation: One standard, many interpretations
A pharmaceutical manufacturer invests €2 million in a new facility that can’t reach ISO 5 certification. A semiconductor fab loses 15 percent of wafers to temperature swings. A cell therapy startup halts production over cross-contamination risks. Different industries. Same root cause: a cleanroom design that didn’t account for the realities of operation, regulation, and workflow.
Every cleanroom begins with ISO 14644-1, the international standard that classifies air cleanliness based on particle concentration. But achieving compliance isn’t simply about hitting particle counts. It’s about how classification, airflow, materials, personnel flow, and monitoring integrate into a system that can sustain control day after day. And that’s where industries diverge. Each sector applies ISO 14644 through its own regulatory lens, creating distinct design challenges that demand more than technical precision. They demand understanding.
Pharmaceutical cleanrooms: the compliance crucible
Few environments are under as much scrutiny as pharmaceutical manufacturing. Here, cleanrooms must meet both at-rest and in-operation standards, forcing HVAC systems to maintain stability even during full production. Airflow, temperature, and pressure differentials must stay within tight limits while operators, materials, and equipment constantly disrupt equilibrium.
Aseptic processing adds another layer. Grade A (ISO 5) zones must deliver unidirectional airflow of at least 0.2 m/s—even around filling lines, isolators, and glove ports. Add to this the need for continuous environmental monitoring, data integrity, and microbial control, and it becomes clear why design can’t rely on generic formulas.
One of the biggest mistakes we see is over-specifying air changes without airflow modeling. Many rooms that technically meet the spec on paper fail certification once real-world conditions are applied. That’s why at Jansen we model airflow using CFD simulation before construction, ensuring compliance that lasts beyond validation day.
Biotech & cell therapy: the flexibility paradox
Cell and gene therapy have redefined what a “cleanroom” means. In these facilities, processes are smaller, faster, and far more personal. Each batch may represent a single patient. Designers must separate autologous workflows to prevent cross-contamination, while keeping layouts flexible enough for rapidly evolving processes.
The challenge is that regulatory frameworks like GMP were never written with advanced therapies in mind. As a result, designers face conflicting rules: GMP pushes for outward air cascades, while biosafety levels (BSL) call for inward containment. Finding the middle ground between contamination control and biocontainment requires deep interdisciplinary expertise.
Time pressure makes it harder. ATMP facilities often need to be operational within months, yet still pass full GMP inspection. Our solution is to build scalable infrastructure from the start (extra mechanical space, modular layouts, and HVAC redundancy) so facilities can evolve without rebuilding. In biotech, speed and compliance must coexist, and the right design makes that possible.
Semiconductor & microelectronics: the sub-micron battlefield
If pharmaceuticals fight microbes, semiconductors battle molecules. Here, a single particle can destroy an entire wafer. That’s why fabs demand ISO 4 to 5 environments with ULPA filtration capable of removing 99.999 percent of 0.12 µm particles. The margin for error is microscopic. Temperature must stay within ± 0.5 °F and humidity within ± 5 percent RH. Electrostatic discharge is an invisible enemy—every surface, from flooring to benches, must dissipate static safely.
Even design geometry matters. Gaps between ceiling filters or oversized light fixtures can cause turbulence that ruins laminar flow. We’ve seen projects lose millions in yield because small layout decisions compromised airflow integrity. In semiconductor design, discipline is the difference between precision and failure.
Healthcare cleanrooms: the patient-safety imperative
Hospitals face a dual challenge: protect the product (medications, instruments) and the patient. Operating theaters, isolation rooms, and compounding pharmacies each require different pressure regimes (some positive, some negative) often side by side.
Unlike manufacturing sites, hospitals can’t shut down for maintenance. Systems must run 24/7 and still meet both ISO 14644 and ASHRAE 170 airflow standards. Lighting, HVAC, and medical utilities compete for ceiling space, and small compromises can have serious clinical consequences. Our designs integrate technical and clinical input from the start. The goal isn’t just compliance, it’s a cleanroom that supports healing, safety, and care continuity.
Universal pitfalls that cross every industry
Across all sectors, the same mistakes reappear:
- Ignoring real heat loads – Cleanrooms generate heat; undersized HVAC means unstable conditions.
- Tight space planning – Always design 10–20 % extra capacity for future expansion.
- Skipping CFD modeling – Guesswork kills certification and inflates energy use.
- Flawed envelopes – Gaps, rivets, and sharp corners become contamination traps.
- Budget myopia – Forgetting lifecycle costs for monitoring, calibration, and filters leads to “cheap” projects that cost more later.
Experience shows: prevention is always cheaper than correction.
The Jansen approach: designing for reality, not theory
Our philosophy is simple: a cleanroom must work on paper, in simulation, and in daily operation. That’s why every Jansen project combines industry-specific expertise, integrated design teams, and operational validation through CFD, mock-ups, and commissioning. From the first sketch to qualification, we design for how your facility will perform, not just how it will test.
Cleanrooms are evolving fast. We see a shift toward modular construction, AI-driven monitoring, and energy-optimized HVAC systems. But one truth endures: no technology replaces understanding. Every successful cleanroom begins with listening to the process, the product, and the people who use it.
Ready to build a smarter, more efficient cleanroom?
At Jansen Cleanrooms & Labs, we design environments where compliance meets energy performance. We combine advanced HVAC strategies, intelligent controls, and lifecycle monitoring to help you reduce operating costs without compromising quality or safety.
Contact our team today to explore how we can support your next energy-efficient cleanroom project.