With the emergence and spread of new methicilin resistant Staphylococcus aureus (MRSA) strains, control of dissemination, both in hospitals and in the community, requires the molecular characterization of the circulating strains in order to establish their dynamics and identify the sources of infection. During this study we analyzed the MRSA isolates by means of PCR-based methods in order to improve epidemiological surveillance and early application of prevention measures. The presence of mecA, nuc, lukF-PV and lukS-PV genes, as well as SCCmec types was assessed in relation to clinical characteristics and multidrug resistance (MDR) for 86 MRSA isolates and showed that 51% of MDR strains were carriers of mobile genetic elements SCCmec IV and the majority of non-MDR SCCmec type IV strains were PVL-positive (81.8%). Comparison of diagnostic methods showed that PBP2 detection represents an extremely useful alternative to PCR for the rapid screening of MRSA isolates, in laboratories that lack facilities necessary for molecular diagnosis, such as PFGE (Pulse Field Gel Electrophoresis), spa-typing and/or MLST (Multilocus Sequence Typing).