The aim of this study was to evaluate the prevalence and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) among pigs and estimate the impact of this animal reservoir on human healthcare. Nasal swabs were derived from 1,600 pigs at 40 German farms. The MRSA were characterized using S. aureus protein A (spa) typing, multilocus sequence typing (MLST) and detection of toxin genes. In a retrospective case control study, we compared risk factors for the carriage of MRSA between patients carrying spa types found among regional pigs and patients with other MRSA molecular types. Pigs carrying MRSA were identified on 70% of the farms (spa types t011, t034, t108, t1451 and t2510, all associated with MLST sequence type ST398). Contact to pigs and cattle were independent risk factors for the carriage of these spa types in patients at hospital admission. Our results indicate that livestock represents a relevant reservoir for the import of MRSA into regional German hospitals.