One of the serious and growing challenges for infection control programs worldwide is hospital acquired infections. Pseudomonas aeruginosa is considered the most common cause of hospital acquired Gramnegative infections. Intensive exposure of hospital pathogens to biocides may result in the emergence of resistance not only to the biocides, but possibly to antibiotics as well. Thus, the current study was done to investigate the prevalence of qacE∆1 and qacE genes and their correlation to antibiotics and biocides resistance in Pseudomonas aeruginosa isolated in Egypt. The antimicrobial activity of six biocides against drug sensitive and multi-drug resistant Pseudomonas aeruginosa was evaluated. Phenol and formalin displayed a higher antimicrobial activity compared to other biocides tested. Minimum inhibitory concentration (MIC) values of chlorine releasing agents were higher than the dilution prescribed by their manufactures. The qacE∆1 gene was identified in 57.8% of multidrug resistant isolates and 21.4% in susceptible strains, While, qacE gene was only detected among multi-drug resistant Pseudomonas aeruginosa. This study reported a correlation between qacE∆1 and multidrug resistance Pseudomonas aeruginosa, while there was no correlation between the presence of qac genes and increased MIC values to biocides. The effectiveness of biocides is very important to control microbial population and prevent the transmission of infections in hospitals. In conclusion we highlight the need for health care facilities to assess the antimicrobial effectiveness of biocides periodically.