We analysed nosocomial MRSA cases between January 2004 and December 2006 in a retrospective case-control study in a 250-bed tertiary-care teaching hospital. During the study period, 265 nosocomial Staphylococcus aureus infections were identified in 231 patients. There was a significant increase in methicillin resistance in isolates (MRSA) from these infections with frequencies for 2004 of 39/88 (44·3%), 2005 (62/80, 77·5%), and 2006 (75/97, 77·3%) (P<0·001). Multivariate analysis showed that associated factors for nosocomial MRSA infection were prolonged hospitalization (OR 3·982, 95% CI 2·235–7·094, P<0·001), mechanical ventilation (OR 3·052, 95% CI 1·666–5·590, P<0·001), surgical operation (OR 2·032, 95% CI 1·102–3·748, P=0·023), and male sex (OR 2·000, 95% CI 1·081–3·699, P=0·027). The determination of associated factors for methicillin resistance in nosocomial S. aureus infections in hospitals will play an important role in efforts to reduce MRSA infection rates.