States across the U.S. lack effective ways to quantify HIV prevalence rates among men who have sex with men (MSM). We estimated population-based HIV prevalence rates among MSM in the 17 southern states by race/ethnicity. Through 2007, estimated HIV prevalence rates per 100,000 MSM ranged from 2,607.6 among white (non-Hispanic) MSM in Maryland to 41,512.9 among black (non-Hispanic) MSM in the District of Columbia. Black MSM rates significantly exceeded Hispanic and white MSM rates in each state. Significant racial/ethnic disparities in rates persisted in a sensitivity analysis examining the possibility that minority MSM populations had been underestimated in each state. Compared with black, Hispanic, and white non-MSM males, respectively, rates at the regional level were 25.2 times higher for black MSM, 43.0 times higher for Hispanic MSM, and 106.0 times higher for white MSM. State-level analysis of racial/ethnic-specific MSM HIV prevalence rates can help guide resource allocation and assist advocacy.