The presence of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals and the community is a serious problem. Accordingly, a comprehensive plan has been implemented in the County of Vejle, Denmark, to identify colonised and/or infected individuals and to control the spread of MRSA. Since 2005, all patients and healthcare personnel have been screened for MRSA colonisation, involving analysis of 300-400 samples daily. To deal with this number of samples, a PCR-based method customised for high-throughput analysis and a system for fast reporting of MRSA carrier status were developed. Swab samples were incubated overnight in a selective tryptone soya broth and were analysed by PCR the following day. Using this strategy, non-colonised individuals were identified within 24 h, while MRSA-positive samples were analysed further by traditional microbiological methods to determine the resistance pattern. This is a cost-effective approach, as the greatest expense in hospitals involves the isolation of patients of unknown MRSA status. The method was evaluated by testing 2194 clinical samples, with a sensitivity and specificity of 100% and 94%, respectively. The analytical sensitivity was 97%, with 161 of 166 different MRSA strains and isolates generating positive results according to PCR analysis. Using four control strains, the inter-assay variation was revealed to be a maximum of 2.6%, indicating good reproducibility.