Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is increasingly common in the USA, but rare in the UK. We compared CA-MRSA from the UK and USA to examine differences in the molecular epidemiology. We investigated patients presenting with MRSA in the first 72 h of hospital admission or in out-patient settings in a UK and a US hospital from January 2004 to March 2006. Fluoroquinolone susceptibility was used as a screening marker to select presumptive CA-MRSA. One hundred and eighteen and 49 such strains were identified, representing a prevalence of 0.1 and 0.2 isolates per 1,000 patient days in the UK and US respectively. Panton-Valentine leukocidin (PVL)-positive ST8-IVa (USA300)-type strains predominated among 43 surviving US isolates, whereas PVL-negative ST1-IVa predominated among 71 surviving UK isolates. There are striking differences between the molecular epidemiology of CA-MRSA in UK and US hospitals, which may have implications for control.