Accumulated data indicate that meticillin-resistant Staphylococcus aureus (MRSA) infections are associated with a worse prognosis than methicillin-susceptible S.aureus infections. To assess the epidemiological profile of S.aureus infections and the genetic diversity of clinical strains of MRSA in 12 hospitals in southern Poland. Samples from bloodstream infections, pneumonia, and skin and soft tissue infections from adult patients were examined. S.aureus isolates were tested for MRSA and macrolide-lincosamide-streptogramin B (MLSB) phenotypes. Staphylococcal cassette chromosome mec (SCCmec) typing and S.aureus protein A (spa) typing were performed. Analysis of the genetic similarity was performed by pulsed-field gel electrophoresis. This study included 555 patients. An MRSA phenotype was detected in 15.1% of strains. The prevalence of MRSA infection was higher in patients aged >80 years. An MLSB phenotype was detected in 18.2% of strains. Analysis of SmaI profiles did not reveal a dominant clone. Spa typing showed 25 different spa types, and spa type t003 was the most common (49% of strains). Among MRSA strains, SCCmecII (49%) and SCCmecIV (27.4%) were predominant. The characteristics of MRSA showed considerable heterogeneity. The results demonstrate the need for caution when drawing conclusions on direct epidemiological relationships between isolates based on a single typing method. As the cases of infection in this study were not associated with the hospital environment and horizontal transfer, a focus on screening at hospital admission, and appropriate infection control, may help to reduce the risk of MRSA infections.