An outbreak of meticillin-resistant Staphylococcus aureus (MRSA) occurred in surgical and internal medicine units of a 1752-bed Finnish tertiary care hospital during 2003-2004. In order to analyse the costs of this 14-month outbreak, patients were categorized as follows: patients with MRSA infections; patients with MRSA colonization; patients exposed to MRSA but whose MRSA status remained inconclusive; and exposed patients who were negative for MRSA. We reviewed a sample of patients' charts to determine the types of clinical infections and interviewed staff about the practical implementation of control measures. The number of patients and patient-days involved in the outbreak were identified from the hospital's databases, with the administrative database supplying unit costs of work and materials. Loss of income due to closed beds was analysed. A total of 266 MRSA-positive patients (114 with infections and 152 colonized) and 797 patients exposed to MRSA were identified (11,744 contact isolation days). There were 1240 patients negative after screening (9880 contact isolation days). Total additional costs of MRSA were 386,062 euro (70% for screening and 25% for contact isolation). Costs due to meticillin resistance in treatment of MRSA infections were 16,000 euro. The income loss for this hospital due to closed beds was 1,183,808 euro. The high cost of MRSA screening underlines the importance of appropriate screening methods. Our model of analysing costs might be useful for other hospitals after adapting variables such as local control measures.