Typing multiply-resistant bacteria using molecular techniques is high priority for national health authorities. Routine typing of meticillin-resistant Staphylococcus aureus (MRSA) was initiated in Austria 2005 and was performed by sequence analysis of the variable X region of protein A gene (spa), characterisation of the mec gene (SCCmec) and testing for Panton-Valentine leukocidin (PVL), enterotoxins, toxic shock syndrome toxin and the epidermolytic toxin genes. Ten different spa types, including newly identified t2023, were found among 66 clinical MRSA isolates originating from two neighbouring hospitals under the same management. Spa type t2023 was initially isolated in December 2005 from hospital A, where it became the dominant spa type during 2006 (nine of 16 isolates). The occurrence of type t2023 in hospital B remained a unique event and could be epidemiologically linked to a patient transferred from hospital A. Spa type t2023 is very similar to spa type t001. An isolate of spa type t001 from hospital A showed an enterotoxin gene pattern, multilocus sequence type (MLST) and SmaI macrorestriction PFGE pattern indistinguishable from that of t2023. Epidemiological differences suggested that infection control measures can prevent MRSA cross-transmission. Hospital B had a more stringent MRSA isolation policy, a higher nurse:patient ratio and provided more resources for infection control than hospital A.