In recent years, the increasing incidence of urinary tract infection (UTIs) caused by Staphylococcus aureus has been noted at the urology ward, Okayama University Hospital. We investigated the molecular epidemiological characteristics of 139 UTI isolates, including 45 methicillin-sensitive S. aureus (MSSA) and 94 methicillin-resistant S. aureus (MRSA), collected over a 10-year period from 1990 to 1999. The antibiotic resistance genes (mecA, aph(3′)-III, aac(6′)-aph(2″), ant(4′)-I) and the toxin genes (tst, sea, seb, and sec) were detected by using multiplex polymerase chain reaction (PCR). Since 1996, the prevalence of the ant(4′)-I, tst and sec genes has increased markedly in coagulase type II S. aureus possessing the mecA gene (MRSA). The presence of toxin genes in MRSA was higher than that in MSSA; 66.0% and 26.7% for tst, 7.4% and 4.4% for sea, 24.5% and 8.9% for seb, and 66.0% and 28.9% for sec, respectively. In the review of medical records, it was found that febrile episodes occurred in 12 of 72 patients with monomicrobial UTI caused by S. aureus. For the febrile patients, S. aureus isolates with both the tst and sec genes were found significantly more often (11 of 12; 91.7%) than those without the tst and sec genes (P= 0.0484). Molecular typing of MRSA isolates, by using random amplified polymorphic DNA analysis and pulsed-field gel electrophoresis analysis, revealed no apparent clonality of these isolates over the 10 years, suggesting that most of the recent MRSA infections are not due to cross-infection in the urology ward.