Pulsed-field gel electrophoresis (PFGE) of SmaI macrorestriction fragments of genomic DNA as well as staphylococcal cassette chromosome mec (SCCmec) typing for mecA-carrying isolates were used to study the distribution of clonal types among 177 Staphylococcus aureus clinical isolates recovered in a Spanish hospital between 2000 and 2003. Five major clonal types (P1 to P5) were identified by PFGE, with one of them (P1) comprising the majority of strains (47.5%). According to SCCmec typing, SCCmec type IVA was the most prevalent type, showing increasing prevalence in the hospital setting with respect to other pandemic clones. One SCCmec pattern was detected in different PFGE types, which demonstrates that the latter is a major discriminative typing method. Three novel SCCmec elements or variants were found, each in a different PFGE type. Oxacillin (methicillin)-resistant and -susceptible S. aureus (MRSA and MSSA, respectively) strains were detected showing identical PFGE patterns, suggesting horizontal transfer of mecA to MSSA and/or mecA deletion from MRSA. Persistence of several S. aureus clones throughout the years within the same hospital environment was also observed. © 2007 Elsevier B.V. and the International Society of Chemotherapy.