HIV-infected individuals, especially those with a history of injecting drug use, are at high risk of Staphylococcus aureus infection. Moreover, the use of antimicrobial agents for opportunistic infections may increase nasal colonization by antimicrobial-resistant Staphylococcus aureus in this population and, subsequently, levels of infection with multidrug-resistant Staphylococcus aureus in the community. Between February 1999 and March 2000, 500 subjects from a community-based cohort of drug users completed an interview and underwent a physical exam. Risk factors for colonization by Staphylococcus aureus were examined, the antibiotic susceptibility profiles of all strains were determined, and DNA strain analysis was performed. One hundred twenty (24%) subjects had positive Staphylococcus aureus nasal cultures. Only HIV infection and homelessness were associated with Staphylococcus aureus colonization. Ten (8%) isolates were methicillin-resistant Staphylococcus aureus. Methicillin-resistant Staphylococcus aureus isolates were found more frequently among HIV-infected than HIV-uninfected respondents (14% vs. 3%, P=0.04). Among those colonized and HIV infected, the mean number of resistant isolates was higher for those currently reporting antibiotic use (5.0 vs. 2.3, P<0.001) and for those with CD4+ counts 200/µl (3.8 vs. 2.3, P=0.02). The increased use of antimicrobial agents in HIV-infected individuals colonized with Staphylococcus aureus may be an underlying mechanism that contributes to the presence of multidrug-resistant Staphylococcus aureus in the community.