This study describes the distribution and frequencies of strain types by protein A-encoding gene (spa) typing among a total of 200 meticillin-resistant Staphylococcus aureus (MRSA) single-patient isolates collected between 2000 and 2005 at the University Hospital Basel, Switzerland. Nine frequent spa types accounted for 49.5 % of MRSA isolates, whereas spa type t041 (15 % of all isolates) belonged to a local epidemic strain that is also a common strain type in southern Germany. Successful control of the outbreak strain was documented by epidemiological data and confirmed by spa typing results. The spa type t044 (3.5 %), corresponding to a widely disseminated European community-acquired MRSA (CA-MRSA), was first observed in 2002. The well-known CA-MRSA USA300 clone was detected in four patients (2 %). Sporadic strains occurring less than four times (32 different spa types) accounted for 23 % of isolates. No predominant spa type was seen, indicating a great genetic diversity. Only 34.5 % of patient isolates were acquired nosocomially. The presence of one or more of ten common virulence genes was shown in 79 % of strains. It was demonstrated that the sequence-based spa typing method allows analysis of local MRSA epidemiology in relation to other regions and countries over time.