How Contamination Happens in Labs (and How to Prevent It)

Contamination is one of the most common—and costly—problems in both life science laboratories and materials research labs. From microbial contamination in cell cultures to compromised results in environmental labs, the risks are the same: inaccurate data, wasted resources, and unnecessary expense. A single misstep in laboratory practices, workflow, or equipment care can cause results to collapse. Since Louis Pasteur’s work in Germ theory disproving spontaneous generation, contamination has been recognized as a critical challenge in science. The good news is that contamination is preventable. This blog explores the main ways contamination happens and provides practical strategies to eliminate contamination risk before it affects your work.

Common Sources of Contamination

Poor and Aseptic Technique

Human error is often the biggest source of contamination. Improper glove use, careless pipetting, or opening sterile containers outside a biological safety cabinet or laminar flow hood can quickly compromise lab samples. Talking over open cell cultures, resting pipettes on benches, or wearing the same personal protective equipment (PPE) between different cell lines are classic examples where lapses in good aseptic technique lead to contamination.

Dirty or Improperly Cleaned Glassware and Tools

Even the smallest residue left on glassware or laboratory equipment can interfere with experiments. Traces of detergents, solvents, or biological contaminants can skew results in sensitive assays. Using improperly rinsed volumetric flasks, failing to wash homogenizer probes or stainless steel probes thoroughly, or neglecting sterilization procedures with deionized water allows residues to build up. This can migrate into new experiments, causing false results and increased contamination risk.

Cross-Sample Handling and Workflow Mistakes

Reusing pipette tips, mislabeling tubes, or failing to separate clean and used areas introduces contamination risks. Handling multiple biological samples at once, preparing Master Mix near aerosolized DNA templates, or using the same mortar and pestle for raw materials from different projects can also lead to cross-sample contamination. Issues like amplification carryover in PCR or technician errors during sample preparation highlight why strict laboratory workflow design and adherence to standard operating procedures are essential.

Environmental Contamination

Airborne dust, aerosols, and microbes can settle onto open lab samples. HVAC units, poorly maintained HEPA filtration systems, or leaving 96-well plates uncovered in high-traffic areas all contribute to contamination. Environmental labs face additional challenges, such as radiation contamination or exposure to hazardous materials. Without HEPA air filters, humidity control, and ISO 14644-compliant environments, background contamination can overwhelm even well-prepared culture conditions.

How to Prevent Contamination in the Lab

1. Plan Your Workflow – Clearly separate clean and dirty zones. A one-way workflow, where samples move only from preparation to analysis without backtracking, minimizes cross-exposure. Lab safety management systems and validation protocols ensure that laboratory personnel follow structured processes.

2. Commit to Aseptic Technique – Aseptic methods protect both samples and researchers. Wearing proper personal protective equipment, practicing Good Pipetting Practice, and following standard operating procedures reduce human-derived contaminants. Using no template controls in PCR and enforcing strict culture conditions strengthens data reliability.

3. Use Sterile Consumables – Pre-sterilized or single-use consumables act as barriers to contaminants. Items such as sterile 96-well plates, Omni Tips, hybrid probes, and single-use homogenizer probes eliminate the variability of in-house cleaning and improve sample integrity.

4. Clean and Calibrate Equipment – Regular cleaning removes residues, while calibration ensures instruments perform reliably. Laboratory high-pressure homogenizers, gas chromatographs, and other complex instruments require cleaning equipment and calibration schedules to avoid hidden contamination.

5. Routinely Sterilize Tools – Autoclaving, UV light, radiation sterilization procedures, or chemical sterilants keep reusable glassware and instruments contamination-free. Sterile filtration is also an effective method for protecting solutions from microbial contamination.

6. Protect Your Samples – Biological samples and cell lines must be stored under the right conditions. Vapor phase storage in liquid nitrogen (LN2), controlled CO2 sensors, and copper internal chambers maintain sample integrity while preventing Mycoplasma contamination. The vapor phase of LN2 storage is especially useful for cell authentication and preservation.

7. Control Your Environment – Laminar flow hoods, flow hoods, and biological safety cabinets protect against airborne contaminants. HEPA filters, HEPA air filters, and ISO 5 cleanrooms provide sterile environments where sensitive laboratory techniques can be performed safely.

8. Minimize Direct Handling – Every physical interaction is an opportunity for contamination. Automated liquid handling systems reduce technician errors and exposure to aerosolized DNA templates, supporting reliable in-process testing.

9. Label and Track Carefully – Accurate, consistent labeling prevents costly mix-ups. Digital tracking, genotypic testing, and shotgun metagenomics approaches ensure culture conditions and cell authentication remain traceable and verifiable.

10. Maintain a Culture of Cleanliness – Cleanliness is not just about surfaces; it is a culture. Routine use of DNA Away™, Odor Neutralizer, and consistent laboratory safety protocols helps reduce biological contaminants. Accountability among laboratory personnel sustains long-term contamination monitoring programs and supports good laboratory techniques.

How Contamination Affects Results

The consequences of contamination extend far beyond a spoiled experiment. Contamination undermines reproducibility, making it difficult for others—or even the same Lab Manager or safety expert—to validate findings. This weakens trust in results and slows scientific progress. Financially, contamination wastes expensive reagents, rare cell cultures, and laboratory personnel time, inflating project costs. In PCR and qPCR, microbial contamination or aerosolized DNA templates can skew Ct values and compromise DNA template analysis. Cell culture contamination, such as Mycoplasma contamination, damages cell lines and invalidates entire studies. More critically, contamination can mislead conclusions, producing false positives or negatives that steer research in the wrong direction. In regulated life science labs and sanitary applications, contamination can halt projects, disrupt in-process testing, and compromise compliance with ISO 14644 or validation protocols. The true cost is not just in dollars but in credibility, safety, and the pace of discovery.

Final Thoughts

Contamination isn’t unavoidable—it’s preventable. By committing to strong laboratory practices, careful workflow planning, and sterilized equipment, labs can minimize risks while maximizing productivity and data accuracy. With the right approach, contamination control becomes a foundation for trustworthy research.

MSE Supplies supports contamination prevention with sterile glassware, centrifuge tubes, laboratory equipment for sample preparation, and single-use consumables. Autoclaves, sterilizers, HEPA filters, and laboratory workflow tools provide dependable decontamination. Clean storage and lab organization solutions further reduce contamination risk, making MSE Supplies a trusted partner for life science labs, environmental labs, and beyond.

Protect your results by exploring sterile consumables, autoclaves, and clean storage solutions at MSE Supplies. Connect with us on LinkedIn and subscribe to our newsletter for more expert insights into lab best practices. Contact us now and partner with MSE Supplies to safeguard the integrity of your work.