Between 2006 and 2009, all MRSA isolates recovered from human patients in Upper Austria were subjected to molecular biological analysis. Whereas the isolate number decreased from year to year, the proportion of the most common sequence types (ST5, ST8 and ST22) as well as the frequency of associated PFGE subtypes and spa-types remained similar. The rate of PVL-positive MRSA increased, whereupon the most common sequence types were ST152, ST8 including clone USA300, ST5, ST777 and ST88. The frequency of ST398 was high (25%) in relation to the PVL-positive clones. Thus, we consider a special focus on community-associated MRSA to be necessary.