Outbreaks of MDR (Multi-drug resistant) organisms in hospitals are a major challenge facing hospitals especially tertiary ones and ICUs (intensive care units) nowadays (Ramirez et al., 2006). Typing of these MDR organisms is very important to trace source of infection to cut losses in the form of mortalities and resources (Messaoudi et al., 2010). Pseudomonas aeruginosa is one of the organisms in which MDR strains spread all over the world (Strateva, 2009). The present study aimed to trace MDR Pseudomonas aeruginosa in Cairo university hospitals by REP-PCR which is one of the molecular typing techniques. Although molecular techniques are numerous ;PFGE (pulsed field gel electrophoresis) is considered as the gold standard while the electrospray ionization mass spectrometry as the fastest, easiest and the most recent method of typing (Nieto et al.,2005). Results of the study revealed that pseudomonas spp. were the third most common gram negative bacilli in hospital acquired infections 19.1% (n=375) preceded by E.coli 51.6% (n=1009) and Klebsiella spp. 26.7% (n=523). Thirty five MDR pseumonades were identified by Disc diffusion from which 23 MDR P.aeruginosa were confirmed by multiplex PCR of the outer membrane lipoproteins. All 23 isolates were belonging to 23 patients having catheter associated urinary tract infection (CA-UTI), from the urosurgery ward. REP-PCR revealed that all isolates were from one clone. In conclusion REP-PCR was found to be a rapid and reliable typing technique for bacteriological strains