An emerging subtype of methicillin-resistant Staphylococcus aureus (MRSA), clonal complex (CC) 398, is associated with animals, particularly pigs. We conducted a matched case-control and a case-case study comparing 21 CC398 case-patients with 2 controls randomly selected from the Danish Civil Registry and 2 case-patients infected with MRSA other than CC398. On farms of case-patients, animals were examined for MRSA. Thirteen case-patients reported pig exposure. Living or working on farms with animals was an independent risk factor for CC398 in the case-control (matched odds ratio [MOR] 35.4, 95% confidence interval [CI] 2.7-469.8) and the case-case study (MOR 14.5, 95%CI 2.7-76.7). History of hospitalization was associated with an increased risk only in the case-control study (MOR 11.4, 95% CI 1.4-94.8). A total of 23 of 50 pigs on 4 of 5 farms were positive for CC398. Our results, corroborated by microbiologic testing, demonstrate that pigs are a source of CC398 in Denmark.