HIV-1 infection continues to spread worldwide, primarily through sexual intercourse. Because semen is a major vehicle for transmission of HIV-1, we evaluated the effects of reverse transcriptase inhibitor therapy on the amount of HIV-1 in semen. The semen and blood of 11 HIV-1-infected men (i.e. treatment group) were collected before the initiation of reverse transcriptase inhibitor therapy and then 8 to 18 weeks after initiation of therapy. The semen and blood of another 11 HIV-1-infected men (i.e., longitudinal group), who were not on or had no change in antiretroviral therapy for at least 2 months before study entry, were collected at approximately 2-week intervals for 10 to 26 weeks. In the treatment group, 82% of the seminal plasma HIV-1 RNA levels decreased from baseline after 8 to 18 weeks of therapy (median reduction of 1.01 log10, p = 0.01), and 100% of the blood plasma RNA levels decreased from baseline over the same period (median reduction of 0.92 log10, p = 0.003). Five of these patients were followed for at least 52 weeks and had a median seminal plasma HIV-1 RNA level of 0.66 log10 below baseline at 1 year. All subjects in the treatment group with positive cultures at baseline (50%) had negative cultures or a lower infectious units per ejaculate at the 8- to 18-week follow-up examinations. The HIV-1 RNA levels in blood and semen of the longitudinal group did not change significantly over 10 to 26 weeks. Initiation of reverse transcriptase inhibitor therapy effectively reduces shedding of HIV-1 in semen and may therefore reduce the spread of infection within populations.