Repetitive sequence-based (Rep)-PCR genotyping as described here is based on the presence of homologues of Mycoplasma pneumoniae repeat-like elements in Staphylococcus. In this study we comparatively evaluated the usefulness of rep-PCR typing with two sets of well-defined collections of Staphylococcus aureus strains. Rep-PCR analysis of the first collection of S. aureus strains (n = 59) and one Staphylococcus intermedius strain showed 14 different rep-PCR patterns, with each pattern harboring 6 to 15 DNA fragments. The discriminatory power of rep-PCR typing compared well to those of arbitrarily primed PCR (average of 20 types) and pulsed-field gel electrophoresis (11 types). S. aureus strain collection I comprised four outbreak-related groups of isolates. The isolates in only one group were found to have identical rep-PCR profiles. However, in an analysis of isolates from three additional independent local outbreaks (n for outbreaks 1 and 2 = 5, n for outbreak 3 = 12), identical rep-PCR types were found among strains isolated during each outbreak. Therefore, we conclude that rep-PCR genotyping may be an easy and fast method for monitoring of the epidemiology of nosocomial Staphylococcus infections. Rep-PCR analysis of strain collection II, which consisted of epidemic and nonepidemic methicillin-resistant S. aureus (MRSA) strains, revealed that a cluster of similar rep-PCR profiles was found among MRSA isolates which were more frequently isolated and which were most often associated with outbreaks.