The spread of meticillin-resistant Staphylococcus aureus (MRSA) is a major problem for both acute care hospitals and among residents in long term care facilities (LTCFs). We performed a cohort study to assess the natural history of MRSA colonisation in LTCF residents. Two cohorts of residents (231 MRSA carriers and 196 non-carriers) were followed up for an 18 month period, with cultures of nasal and decubitus ulcers performed every six months. In the MRSA carrier cohort, 110 (47.8%) residents had persistent MRSA colonisation for six months or longer, 44 (19.0%) had transient colonisation and nine (3.9%) were intermittently colonised. No risk factors for persistent MRSA colonisation could be determined. The annual incidence of MRSA acquisition was around 20% [95% confidence interval (CI): 14.3-25.5]. Antibiotic treatment was independently associated with MRSA acquisition (odds ratio: 2.27; 95% CI: 1.05-4.88; P=0.03). Just two clones were distinguishable by pulsed-field gel electrophoresis and multilocus sequence typing: CC5-MRSA IV, which is widely disseminated in Spanish hospitals, and ST22-MRSA IV. This study adds to the knowledge of the epidemiology of MRSA in community LTCFs, which are important components of long term care in Spain.