BackgroundHepatitis C virus (HCV) infection is a widespread problem in prisons. The present study aimed to assess the prevalence of HCV seropositivity, HCV genotypes, factors associated with HCV seropositivity in newly incarcerated prisoners and to report experiences of treatment with pegylated interferon/ribavirin for HCV-positive inmates.MethodsPatient data were extracted from the Estonian prison medical information system (Vanglate meditsiiniline infosüsteem) databases.ResultsAmong 1845 prisoners newly incarcerated from January 2014 to January 2015, the overall prevalence of HCV was 56.3% (95% CI: 54 to 59), and 25.5% (95% CI: 23.5 to 27.6%) had HIV (39.0% had neither). The all-inclusive HCV testing strategy identified 37.7% more HCV infected prisoners than the risk-based (drug use history, HIV status) case finding. Factors associated with HCV seropositivity included history of drug use (aOR 6.51 95%CI 5.12–8.28), HIV co-infection (aOR 2.56 95%CI 1.92–3.43), previous incarceration (aOR 3.61 95%CI 2.48–4.04), and increasing age. The main HCV genotypes were 3a (n = 172, 44.4%) and 1b (n = 135, 35.2%). Twenty-five prisoners received HCV treatment: 60% (n = 15) were cured, 16% (n = 4) relapsed (3 with genotype 3a, one with 1b), and 12% (n = 3) were unresponsive (all with genotype 3a).ConclusionsHCV seropositivity rate is high and HCV tretment rate is very low in Estonian prisons. Optimizing case finding and scaling up treatment is critical to addressing the health needs of prisoners and meeting public health goals.