Biocides have an important role in hospital infection control. The widespread use of biocides may lead to microbial resistance, in particular cross-resistance to antibiotics. The aim of the present study is to determine the qacE Delta 1 gene, which has been known as a determinant of resistance to quaternary ammonium compound (qac), by polymerase chain reaction (PCR) in clinical isolates of multi-drug resistant (MDR) gram negative bacteria. Also, quantitative suspansion test were performed for fenotypic susceptibility to an qac disinfectant in gene positive isolates. Specific primers were used to amplify a 300 bp fragment of qacE Delta 1 gene. The results of the present study may contribute to distribution of qacE Delta 1 gene in our hospital isolates.