Stenotrophomonas maltophilia is an emerging multidrug-resistant global opportunistic pathogenand isacquiring increasing importance as a nosocomial pathogen. This study aimed to determine the prevalence of nosocomial S. maltophilia infections and the important risk factors associated with such infections in Assiut University Hospitals. This study included 362 patients with nosocomial infections admitted to different wards and intensive care units (ICU) from March 2011 to March 2012. A total of 690 different clinical samples according to the site of infection were collected from them. The samples were processed and diagnosed by conventional bacteriological methods. A total of 35 strains of S. maltophilia were isolated from 362 patients (9.6%). The commonest clinical manifestations were lower respiratory tract infections (71.43%), wound infections (17.14%), bacteraemia (8.57%) and urinary tract infections (2.86%). The chest ICU showed the highest percentage of isolation (14.75%). Previous antibiotic intake was found to be a significant risk factor for nosocomial Stenotrophomonas maltophilia infections. We conclude that nosocomial Stenotrophomonas maltophilia infections are significant in Assiut University Hospitals with lower respiratory tract infections being the commonest and previous antibiotic intake an important risk factor.