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HIV incidence in the United States among men who have sex with men (MSM) has been increasing since 2000, and MSM remain the most heavily impacted risk group in the US HIV epidemic.We modeled HIV transmissions, using data from MSM in five US cities from the National HIV Behavioral Surveillance System, the HIVNET Vaccine Preparedness Study, and other published data. Annual HIV transmissions were estimated by partner type (main or casual) and by sex type (receptive anal intercourse, insertive anal intercourse, or oral sex).Sixty-eight percent [95% confidence interval (CI) 58–78) of HIV transmissions were from main sex partners because of a higher number of sex acts with main partners, more frequent receptive roles in anal sex with main partners, and lower condom use during anal sex with main partners. By sex type, 69% (95% CI 59–79) of infections were from receptive anal intercourse, 28% (95% CI 19–38) were from insertive anal intercourse, and 2% (95% CI 0–5) were from oral sex. The model-based estimated HIV incidence rate was 2.2% (95% CI 1.7–2.7) per year. Sensitivity analyses demonstrated estimates of transmission from main sex partners as low as 52% (95% CI 41–62) and as high as 74% (95% CI 68–80).According to our model, most HIV transmissions among MSM in five US cities are from main sex partners. HIV prevention efforts should take into account the risks of HIV transmissions in male partnerships, and couples-based HIV prevention interventions for MSM should be given high priority in the US HIV prevention research portfolio.