Background HIV prevalence among men who have sex with men (MSM) is thought to be high in Jamaica. The objective of this study was to estimate HIV prevalence and identify risk factors in order to improve prevention approaches. Methods With the help of influential MSM, an experienced research nurse approached MSM in four parishes to participate in a cross-sectional survey in 2007. MSM were interviewed and blood taken for HIV and syphilis tests, and urine taken for gonorrhoea, Chlamydia and Trichomonas testing using transcription-mediated amplification assays. A structured questionnaire was administered by the nurse. Results One third (65 of 201; 32%, 95% Confidence Interval (CI) 25.2% – 47.9%) of MSM were HIV positive. Prevalence of other sexually transmitted infections (STI) was: Chlamydia 11%, syphilis 6%, gonorrhea 3.5% and Trichomonas 0%. One third (34%) of MSM identified themselves as being homosexual, 64% as bisexual and 1.5% as heterosexual. HIV positive MSM were significantly more likely to have ever been told by a doctor that they had a STI (48% vs. 27%, OR 2.48 CI 1.21 – 5.04, p=0.01) and to be the receptive sexual partner at last sex (41% vs. 23%, OR 2.41 CI 1.21 – 4.71, p=0.008). MSM who were of low socio-economic status, ever homeless and victims of physical violence were twice as likely to be HIV positive. The majority (60%) of HIV positive MSM had not disclosed their status to their partner and over 50% were not comfortable disclosing their status to anyone. Conclusions The high HIV prevalence among MSM is an important factor driving the HIV epidemic in Jamaica. More effective ways need to be found to reduce the high prevalence of HIV among MSM including measures to reduce their social vulnerability, combat stigma and discrimination and empower them to practice safe sex.