Contradictory results are reported for the behaviour of quaternary ammonium compounds (QACs) in sewage treatment plants (STPs). QACs may sorb onto activated sludge. Only little information is available with respect to effects of QACs against bacteria in STPs. Only 5 to 15% of bacteria present in sewage sludge can be detected by means of culture dependent microbiological methods. The shift of the bacterial populations due to effects of test compounds have not been studied up to now with culture independent methods. The microbial populations shift was studied in situ using culture independent chemotaxonomy profiling ubiquinones and polyamines. Additionally, toxic effects of QACs against bacteria present in the test vessels of the Zahn-Wellens test (OECD 302 B) were assessed with a toxicity control in the test. The ubiquinone profiles representing changes in Gram-negative populations mainly showed that the activated sludge was affected only in test vessels containing benzalkonium chloride. According to chemotaxonomy Acinetobacter or/and some members of Pseudomonas spp. have been selected by benzalkonium chloride after some adaptation period (8 to 12 days)