Population-based estimates of human immunodeficiency virus (HIV) prevalence and risk behaviors among men who have sex with men (MSM) are valuable for HIV prevention planning but not widely available, especially at the local level. We combined two population-based data sources to estimate prevalence of diagnosed HIV infection, HIV-associated risk-behaviors, and HIV testing patterns among sexually active MSM in New York City (NYC). HIV/AIDS surveillance data were used to determine the number of living males reporting a history of sex with men who had been diagnosed in NYC with HIV infection through 2002 (23% of HIV-infected males did not have HIV transmission risk information available). Sexual behavior data from a cross-sectional telephone survey were used to estimate the number of sexually active MSM in NYC in 2002. Prevalence of diagnosed HIV infection was estimated using the ratio of HIV-infected MSM to sexually active MSM. The estimated base prevalence of diagnosed HIV infection was 8.4% overall (95% confidence interval [CI] = 7.5-9.6). Diagnosed HIV prevalence was highest among MSM who were non-Hispanic black (12.6%, 95% CI = 9.8-17.6), aged 35-44 (12.6%, 95% CI = 10.4-15.9), or 45-54 years (13.1%, 95% CI = 10.2-18.3), and residents of Manhattan (17.7%, 95% CI = 14.5-22.8). Overall, 37% (95% CI = 32-43%) of MSM reported using a condom at last sex, and 34% (95% CI = 28-39%) reported being tested for HIV in the past year. Estimates derived through sensitivity analyses (assigning a range of HIV-infected males with no reported risk information as MSM) yielded higher diagnosed HIV prevalence estimates (11.0-13.2%). Accounting for additional undiagnosed HIV-infected MSM yielded even higher prevalence estimates. The high prevalence of diagnosed HIV among sexually active MSM in NYC is likely due to a combination of high incidence over the course of the epidemic and prolonged survival in the era of highly active antiretroviral therapy. Despite high HIV prevalence in this population, condom use and HIV testing are low. Combining complementary population-based data sources can provide critical HIV-related information to guide prevention efforts. Individual counseling and education interventions should focus on increasing condom use and encouraging safer sex practices among all sexually active MSM, particularly those groups with low levels of condom use and multiple sex partners.