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In 2007, incarcerated persons accounted for 0.41% (approximately 16,500) of the Croatian population. In the heterogeneous structure of the prison population in Croatia, some 25%-30% of the prisoners are drug abusers. In this study, we intended to determine precisely the structure of the prison population in Croatia and the prevalence of HBV and HCV markers in this population. It is well known that HBV and HCV infection can spread within prisons, and therefore we tried to determine the rate of acute HBV and HCV infection among prisoners in Croatian prisons. In total, 25.7% of prisoners were positive for some viral hepatitis markers (HBV 11.3%, HCV 8.3%, and HBV/HCV 6.3%). The rate of HBV infection was very high among intravenous drug users (26.2%) and relatively high among highly promiscuous individuals (19.9%). HCV infection was most prevalent among intravenous drug users (50.2%) and relatively high among highly promiscuous individuals (7.5%). HBV/HCV coinfection was recorded in 23.5% of prisoners. Acute infection with HBV was detected in 0.3% and with HCV in 1.2% of the study population. One fourth of all prisoners had contact with HBV, HCV, or both viruses. It is evident that both hepatitis virus infections (HCV more and HBV less) are spreading within prisons among prisoners. The opportunity of screening, testing, vaccination, treatment and education of high-risk individuals while they are in the controlled environment of a correctional facility is a good policy for both individuals and the community.