A prospective cohort study including all new cases of methicillin-resistant Staphylococcus aureus (MRSA) colonization or infection in 64 Spanish hospitals during June 2003 was performed to investigate the epidemiology of MRSA in Spain. Only patients who yielded clinical MRSA-positive samples were included. Epidemiological and clinical data for a total of 370 cases were collected. Genotyping was performed using pulsed-field gel electrophoresis and multilocus sequence typing. Panton-Valentine leukocidin genes and the staphylococcal chromosomal cassette mec (SCCmec) were identified in representative isolates. MRSA was considered to be nosocomially acquired in 202 cases (55%), healthcare-associated (HCA) in 139 cases (38%), community-acquired (CA) in three cases, and of uncertain mode of acquisition in 26 (7%) cases. The pooled population-based rate was 2.31 cases/100,000 population/month, and the pooled nosocomial rate was 0.21 cases/1000 hospital stays (20.2% of S. aureus). Peripheral vascular disease, respiratory tract infections, catheter infections, bloodstream infections and crude mortality were more frequent among HCA cases, whereas neoplasia and urinary tract infections were more frequent among nosocomially acquired cases. Two clones related to the paediatric clone ST5-IV accounted for 71% of the isolates; EMRSA-16 has emerged in two different geographical areas. Only one isolate belonged to the formerly predominant Iberian clone. The three CA isolates were related to the USA300 clone. SCCmec type IV was the most frequent type in nosocomial and HCA isolates. The epidemiology of MRSA has changed in Spain; outpatients with previous healthcare contact represent a very important reservoir of MRSA, and community isolates are emerging.