Western Siberia is the region with little information on the prevalence of hepatitis C virus (HCV) infection, genotypic diversity of HCV isolates and risk factors. A molecular epidemiological survey was conducted to clarify these issues. Four groups of volunteers were included in a cross-sectional study (n = 500 in each group): health care workers; daycare patients from a hospital for drug users, daycare patients from an AIDS prevention and control center; and persons admitted to a local general practice clinic for any reason (outpatients). The anti-HCV IgG prevalence was 4.6% in health care workers, 48.0% in a narcological center, 35.8% in AIDS center, and 5.6% in outpatients. HCV RNA was found in 79.3%–86.3% of seropositives. A total of 388 HCV isolates were genotyped by direct sequencing and phylogenetic analysis of the 5′-UTR and NS5B regions of HCV genome. The genotypes distribution was: 1b—50.3%, 2a—4.4%, 2c—0.3%, 3a—44.8%. One isolate (0.3%) could not be typed unambiguously. This genotypic diversity is intermediate between that of European Russia and China. Genotype 1 prevailed in an older age group (75% among 51–60 years old), and genotype 3 was most prevalent in young people (51.4% in 16–20 years old). A statistically significant (P < 0.05) increase in risk was found in intravenous drug users (odds ratio (OR) = 77.5), unemployed persons (OR = 16.3), persons having >4 sexual partners during lifetime (OR = 4.3), and male homosexuals (OR = 6.6). J. Med. Virol. 77:382–389, 2005. © 2005 Wiley-Liss, Inc.