Background Evidence is increasing of high HIV risks among southern African men who have sex with men (MSM). This represents the first study of HIV risks and human rights contexts among MSM in Lesotho. Methods Two hundred and fifty-two men who reported ever having anal sex with another man were accrued with snowball sampling and were administered a structured quantitative instrument in October and November 2009. Results Of the participants, 96.4% (240/249) were ethnic Basotho with a mean age of 26.3 years (range 18-56), 49.6% (124/250) were currently employed, and 95.2% (238/250) had at least a secondary-level education. Self-reported HIV prevalence was 11.6% (22/190); 54.5% (128/235) reported being tested for HIV in the last year. HIV knowledge was low; only 3.7% (8/212) of MSM knew that receptive anal intercourse was the highest risk for HIV and that a water-based lubricant was most appropriate to use with condoms. Bivariate associations of wearing condoms during last intercourse with men include: having easy access to condoms (OR 3.1, 95% CI 1.2-8.5, p < 0.05); being older than 26 years (OR 2.3, 95% CI 1.3-4.2, p < 0.01); knowing that receptive anal intercourse is higher risk than insertive anal intercourse (OR 2.6, 95% CI 1.2-5.9, p < 0.05); wearing condoms with female sexual partners (OR 3.5, 95% 1.4-8.3, p < 0.01); using water-based lubricants (OR 2.8, 95% CI 1.4-5.5, p < 0.01); being less likely to report having been diagnosed with a sexually transmitted infecton (OR 0.21, 95% CI 0.06-0.76, p < 0.05); and being more likely to have been tested for HIV in the last year (OR 2.0, 95% CI 1.2-3.6, p > 0.05). Human rights abuses were common: 76.2% (170/223) reported at least one abuse, including rape (9.8%, 22/225), blackmail (21.3%, 47/221), fear of seeking healthcare (22.2%, 49/221), police discrimination (16.4%, 36/219), verbal or physical harassment (59.8%, 140/234), or having been beaten (18.9%, 43/228). Conclusions MSM in Lesotho are at high risk for HIV infection and human rights abuses. Evidence-based and rights-affirming HIV prevention programmes supporting the needs of MSM should be developed and implemented.