An increasing number of reported detections of methicillin-resistant Staphylococcus aureus (MRSA) in food animals since 2007 has led to the assumption that there is an emerging zoonotic problem with livestock associated (la)MRSA potentially aggravating the MRSA problem in humans. It was the objective of the study to investigate, whether MRSA was present in clinical specimens of pigs collected at post-mortem since 2004 and to further characterize these isolates. We studied 138 isolates of S. aureus collected between 2004 and 2007 from various pathological lesions of pigs at necropsy. Potential MRSA were identified by growth on selective chromogenic media. Isolates were confirmed as MRSA using multiplex PCR. Confirmed isolates were spa- and SCCmec-typed and were tested for antimicrobial resistance. Overall, 60 (43%) S. aureus isolates were identified as MRSA. The majority (57/60) of the MRSA isolates found in the altered porcine tissues were spa-types associated with MRSA ST398. Three MRSA were ST97 isolates, a type that has not been described as an MRSA in pigs before. Other clonal complexes (ST9, ST30) dominated among the methicillin-sensitive S. aureus. MRSA were found in similar frequency in all 4 years. We assume that MRSA in pigs may have occurred earlier than 2004 and might be not really ‘emerging’, but rather have been overlooked until recently. The potentially causative role of the MRSA in the lesions warrants further investigation.