Cytomegalovirus (CMV) isolates from 234 asymptomatic human immunodeficiency type 1 (HIV-1)-positive men were analyzed for molecular relatedness using junctional hybridization. Of isolates shed simultaneously at two or more body sites, 36% from 22 men were different. Of 180 isolates collected from 67 men over 15 months, different strains were isolated serially from 27 men (40%), most from semen. After follow-up of 58 months (mean), the relative hazard of HIV infection progressing to AIDS was 1.8 (95% confidence interval [CI], 0.9-3.7) for men shedding the same strain of CMV and 3.0 (95% CI, 1.4-6.1) for men shedding different strains compared with men not shedding CMV in semen. The prevalence of CMV-specific IgM was higher in men shedding different versus same CMV strains (32% vs. 18%; P = .244). Thus, presence of multiple CMV strains in HIV-1-positive homosexual men is associated with progression to AIDS, possibly via activation of HIV-1-infected CD4 cells.