Incarcerated persons comprise about 0·4% of the Croatian population, of whom 25–30% misuse drugs. We attempted to determine the structure of the prison population, prevalence of HBV, HCV, HIV markers, co-infections with HBV, HCV and HIV and acute HBV, HCV and HIV infection. In total, 25·9% of prisoners were positive for some markers for viral hepatitis (HBV 11·3%, HCV 8·3%, HBV/HCV 6·3%). Prevalence of HBV infection in intravenous drug users (IDUs) was 26·2% (highly promiscuous group 20·4%, individuals with psychiatric diseases and personality disorders 16·0%). HCV infection in IDUs was 52·0% and 4·9% in the highly promiscuous group. HBV/HCV co-infection was registered in 34·9% of prisoners positive for HBV markers (203/582). Acute HBV infection was detected in 0·5%, and HCV in 1·2%. Only 0·15% (5/3348) of prisoners were anti-HIV positive. It appears that individuals with psychiatric diseases and personality disorders could be an additional risk population for these viral infections.