A retrospective population-based study of genotypes of methicillin-resistant Staphylococcus aureus (MRSA) was performed during the period 1991-2003 in two counties in the south-eastern part of Norway. Isolates of MRSA from all individuals in the two counties in whom MRSA was detected were genotyped by means of multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A gene (spa) typing and amplified fragment length polymorphism (AFLP) analysis. Until 1999, only sporadic cases of MRSA infection were reported in these counties, but the incidence increased during the following years. Nine new MLST types were identified in this study. The predominant strains were ST239-MRSA-III, the novel ST125-MRSA-IV, and the central European community-acquired strain ST80-MRSA-IV reported previously. ST80-MRSA-IV was introduced into the two counties in 1997, and the incidence of infections has increased since 2000, so that ST80-MRSA-IV is now the commonest MRSA strain in the region. An increase in MRSA clones carrying SCCmecIV has occurred during recent years, which could indicate a shift in the MRSA population in Norway from hospital-acquired MRSA to community-acquired-MRSA.