From 25 June to 11 July 2008, a total of 177 adult patients hospitalised in an intensive care unit (ICU) (94 in medical ICUs and 83 in surgical ICUs) at a tertiary care hospital were screened for nasal carriage of meticillin-resistant Staphylococcus aureus (MRSA) by polymerase chain reaction. The overall prevalence of S. aureus and MRSA nasal carriage among the patients was 42% and 32%, respectively. MRSA carriage rate of the patients hospitalised in medical ICUs was significantly higher than that of those hospitalised in surgical ICUs (47% vs 16%, P<0.001). Multivariate logistic regression analysis revealed that pneumonia, chronic obstructive pulmonary disease, current MRSA infection, and medical ICU admission were independent predictors for nasal carriage of MRSA. Of the 38 MRSA isolates available for molecular analysis, a total of six pulsed-field gel electrophoresis (PFGE) patterns with two major patterns (F, 42%; A, 37%) were identified. Most MRSA isolates belonged to one of two major clones characterised as sequence type 5/PFGE F/staphylococcal cassette chromosome mec (SCCmec) II/Panton-Valentine leucocidin (PVL) genes negative (34%) and ST239/PFGE A/SCCmec III/PVL negative (26%), both clones being associated with healthcare-associated (HA) clones in Taiwan. Six isolates (16%) were characterised as ST59/SCCmec IV or V(T) and were associated with community strains in Taiwan. In conclusion, 32% of ICU hospitalised adult patients in a Taiwanese tertiary care teaching hospital between June and July 2008 were colonised with MRSA in their nares. Though most isolates were HA-MRSA, community strains accounted for a proportion of the isolates.