The number of patients infected/colonised by methicillin-resistant Staphylococcus aureus (MRSA) began to rise in southern Stockholm in 2000. The present study is an analysis based on information concerning the 181 newly detected patients with MRSA during 2000-2003, results of antibiotic susceptibility tests, molecular epidemiologic typing with pulsed-field gel electrophoresis and multilocus sequence typing, and detection of Panton-Valentine leukocidin genes. No single MRSA clone was causing the epidemic situation. Instead a number of rather small, limited outbreaks took place, caused by different MRSA clones and often starting from a patient who had acquired MRSA abroad. Different clones were found in the hospitals and in the community. Sequence types (STs) 22, 239, 247, 8, and 45 were the predominant clones causing outbreaks among hospitalized patients. Most isolates belonging to these clones were multiply resistant to antimicrobial agents. Suspected glycopeptide heteroresistance was found in isolates belonging to STs 247, 239, and 592. In the community, the most widely spread MRSA was ST 80, although isolates belonging to STs 8, 30, 59, and 150 were also observed. The community-acquired isolates were usually not multiresistant. In contrast to the clones transmitted in hospitals, most community-acquired MRSA clones harbored the PVL genes, except for isolates belonging to ST 150 spread in the community among homeless people with foot ulcers and wounds.