This article describes current trends of HIV/AIDS and related conditions in Estonia, with the aim of highlighting key determinants in transmission dynamics and risk groups, problems and barriers of combating HIV/AIDS, and possible implications for prevention and control. Throughout the transition period Estonia has experienced major changes in political, economic, and social structure which all have contributed to increased violence, high-risk sexual behaviour, and substance abuse. Incidences of hepatitis B, C and sexually transmitted infections (STIs) increased in the early 1990s. HIV outbreaks were first detected among injecting drug users (IDUs) in 2000 and are still concentrated among this population group. High rates of sexual risk behaviour and inadequate knowledge regarding prevention of disease transmission in Estonia emphasizes the threat of a sex-related and STI facilitated driven HIV epidemic. To prevent further spread of HIV it is necessary to implement harm reduction interventions among IDUs. However, without effective management of socioeconomic and administrative barriers to health care and other services, an explicit policy on drugs will not reach marginalized groups and will not be able to prevent a further spread of these interrelated epidemics.