To gain information on laboratory hygiene in contained-use laboratories, a method was developed to study the presence of microorganisms on laboratory equipment. Focusing detection on genetically modified organisms (GMOs) containing the universal M13 primer binding sites enabled the detection of a broad range of GMOs using a single PCR. Swabbing surfaces in three different contained-use laboratories led to detection of M13-containing PCR products in 26 out of 34 swabs. Most sequences (up to five per sample) were detected in swabs from the centrifuge and sink, followed by swabs taken from the bin and incubator (up to four sequences per sample). The obtained sequences varied in length from 171 nucleotides (nt) to 878 nt. In most cases, sequences were only partially similar to sequences published in GenBank. The lengths of the regions with high similarity varied from 94 nt to 795 nt, and these similarities ranged from 81% to 100%. Similarities with more than one sequence were commonly found, complicating the identification of detected sequences. Nonetheless, 84% of the detected sequences were actually handled in the laboratory at the time of sampling. This demonstrates that the method may be used as a quality control tool to assess the efficacy of decontamination and cleaning of commonly used surfaces, such as laboratory benches, freezer doors, and centrifuge rotors, without prior knowledge of the identity or characteristics of the GMOs.