This paper examines challenges obtaining representative samples of males who have sex with males (MSM) in Estonia and provides descriptive HIV behavioral data gathered from four cross-sectional surveys; three using the internet, and one using respondent driven sampling (RDS) to recruit MSM in Tallinn and Harju County. Estonian MSM were sampled between March and May in 2004 (n=193), August and November in 2005 (n=146) and September and December in 2007 (n=238) using internet websites. MSM in Tallinn and Harju County were sampled between April and June in 2007 (n=59) using RDS. Recruitment of MSM using RDS did not acquire the calculated sample size. The RDS study reached a less diverse group of MSM than did the internet studies which recruited a larger proportion of MSM who were older, bisexual, having female sexual partners during the last six months, and unlikely to have been tested for HIV. The findings and observations presented in this paper could inform researchers in Estonia, and the region, about the efficacy of and socio-cultural challenges to sampling MSM to collect HIV biological and/or behavioral data.