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The clonal structure of the methicilin-resistant Staphylococcus aureus (MRSA) population in Poland has been analyzed in several reports since the mid-1990s. The present study was performed on 253 MRSA isolates (146 archival and 107 new isolates) recovered in 26 hospitals between 1990 and 2001. Whereas all isolates were typed by pulsed-field gel electrophoresis (PFGE) and the analysis of the ClaI::mecA and ClaI::Tn554 RFLP polymorphism, selected isolates were also subjected to multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) comparisons. Based on the PFGE data, 15 MRSA clones were discerned, seven of which were observed in multiple hospitals. Five of these were related to the pandemic Hungarian (MLST clonal complex, CC8), Iberian (CC8), Pediatric (CC5), Mexican (CC30), and Brazilian clones (CC8). MLST confirmed the earlier reports on the similarity of the Hungarian and Brazilian clones, and it revealed that one of the two remaining epidemic clones was related to the Hungarian/Brazilian, and the other— to the Berlin clones. A local strain from the Northeastern part of the country was found to be similar to a minor Greek clone. The MRSA clonal structure and the increasing complexity of the relationships between the genetic and phenotypic traits of this micro-organism in Poland has now been firmly established.