We found a high prevalence of HIV among injecting drug users (IDU) 54% in Tallinn and 90% in Kohtla Jarve, Estonia. Risk factors for HIV in Tallinn included use of the drug ‘china white’, being registered as an IDU at a drug treatment clinic, and sharing injecting equipment with sex partners. Differences existed in risk behaviour between the cities. An urgent scale-up of HIV prevention is needed. It is also important to explore how local ‘risk environments’ mediate the risk of HIV transmission.