To evaluate the actual burden of methicillin-resistant Staphylococcus aureus and determine risk factors for carriage and infection, we performed a prevalence survey with a nested case-control study among inpatients in Dutch hospitals. The prevalence of carriage was 0.94 cases per 1,000 inpatients, and the prevalence of infection was 0.21 cases per 1,000 inpatients. Professional contact with livestock and a stay in a foreign hospital were associated with carriage.