Surveillance for methicillin-resistant Staphylococcus aureus (MRSA) at the University Hospital of Heidelberg revealed an increase in the numbers of newly detected MRSA isolates in recent years. We conducted a study to assess the dynamics of the changes in the MRSA population. Pulsed-field gel electrophoresis (PFGE) typing of MRSA isolates from all patients at the University Hospital of Heidelberg collected between 1993 and 2004 was performed. The microbiology database contained 1,807 entries for newly detected MRSA isolates from 1,301 patients. A total of 1,252 isolates were available for PFGE typing. The isolates could be classified into 109 different PFGE types. Most PFGE types (n=70) were detected less than five times and showed no evidence of transmission (sporadic strains). They accounted for 8.7% of all isolates, with few variations in frequency over the time. Thirty-seven PFGE types were clustered by time of detection, and transmission of the strains was likely (local epidemic strains). A total of 37.3% of the isolates belonged to this group of strains. The remaining 54.0% of the isolates belonged to only two further PFGE types (endemic strains). One endemic strain accounted for 5.0% of all isolates in 1994 and 68.2% in 2004. A second endemic strain was detected in 1.1% of all isolates in 1998 but in 12.4% in 2004. Statistical analysis of the associations between the kind of strain (sporadic, local epidemic, or endemic) and the patients' characteristics revealed a significant association for age and mode of acquisition. The remarkable increase in the rate of MRSA detection at the University Hospital of Heidelberg is mainly due to the dissemination of two different strains. Infection control measures seemed sufficient to prevent further transmission of some but not all of the strains.