We performed a retrospective cohort study of human immunodeficiency virus (HIV)-associated Mycobacterium avium complex (MAC) infection during 1997-2004 to assess for factors associated with initial macrolide resistance. Of 52 HIV-associated sterile-site MAC isolates, 9 (17%) were initially macrolide resistant. Prior MAC treatment and prolonged MAC prophylaxis with macrolides were associated with infection with a macrolide-resistant isolate; 2 (22%) of 9 patients had limited or no prior macrolide exposure. Initial MAC isolates in HIV-infected persons should routinely be tested for macrolide resistance.