We evaluated the annual and weighted incidence of methicillin-resistant Staphylococcus aureus infections by specific risk factors in a prospective cohort of HIV patients. We found 228 infections in 167 patients from 2002 to 2009. Higher rates were seen in men who have sex with men and intravenous drug users, patients with lower CD4 cell counts, patients not on antiretrovirals and younger patients. The annual incidence peaked in 2007 and has decreased since.