A point-prevalence study, performed in 2002 in 143 Spanish hospitals, collected 439 isolates of Staphylococcus aureus. Of these, 134 (30.5%) were resistant to methicillin (i.e., MRSA). Susceptibility testing was performed by a microdilution method, and mecA was detected by PCR. The isolates were characterised by phage typing, pulsed-field gel electrophoresis (PFGE) after SmaI digestion, and SCCmec typing. The 134 MRSA isolates showed resistance to ciprofloxacin (93.3%), tobramycin (88.8%), erythromycin (67.9%), clindamycin (59.7%), gentamicin (42.5%), mupirocin (17.9%), rifampicin (5.2%) and trimethoprim–sulphamethoxazole (5.2%). All of the isolates were susceptible to glycopeptides. Twenty-five resistance patterns were found, of which four accounted for 66% of the isolates. Phage group III was the most frequent (41.1%). PFGE revealed 31 different patterns, with ten major clones (including two predominant clones with variable antibiotypes that accounted for 43.3% of the MRSA isolates) and 21 sporadic patterns. Two isolates belonged to two variants of the Iberian clone (ST247-MRSA-I), one to the Brazilian clone (ST239-MRSA-III), and seven to the EMRSA-16 clone (ST36-MRSA-II). SCCmecIV accounted for 70.2% of the isolates (73.9% were type IVA), while SCCmecI, SCCmecII and SCCmecIII accounted for 22.1%, 6.9% and 0.8% of isolates, respectively, with three non-typeable isolates. Isolates of SCCmecIV and SCCmecIVA were predominantly nosocomial (95.8% and 97.1%, respectively). None of the isolates produced Panton–Valentine leukocidin. Thus, two clones carrying SCCmecIV and SCCmecIVA, respectively, were predominant among nosocomial MRSA isolates throughout Spain.