This study examines HIV risk behaviour knowledge, substance use and unprotected sex in a sample of 79 men who have sex with men (MSM) in Tallinn, Estonia. Median age of the study population was 30 years (range 18-62 years); 35 were bisexual; 56 answered correctly to at least 10 out of 13 questions about HIV risk behaviours; 23 consumed more than seven alcoholic drinks in the week before the survey; nearly half (n=34) of the participants reported some illicit drug use in the past 12 months; 40 did not use a condom regularly in the 12 months preceding the survey, and 41 did not use a condom during their last sexual intercourse. Alcohol consumption in the week before the survey was negatively associated with condom use during last intercourse (RR 0.48; 95% CI 0.41-0.56). Use of illicit drugs varied significantly by ethnicity (p-value = 0.02). Multivariable analysis showed that higher consumption of alcohol in the week before the survey could be predicted by education, age group and sexual orientation. In conclusion, socio-demographic factors such as education, age, ethnicity and sexual orientation may affect HIV risk behaviour knowledge, sexual behavior and substance use among MSM in Estonia, and need to be taken into consideration for targeted HIV prevention.