Chronic hepatitis C virus infection is one of the most important public health problems. The data published in the Estonian specialist literature until now describe mostly the clinical manifestation and treatment issues of chronic hepatitis C. The present paper gives an overview of the hepatitis C virus, its genome organization and genotypes in Estonia. HCV genotypes were determined in hepatitis C virus-positive patients’ sera in two different periods of time: 1997–1998 and 2000–2004. The results of our studies demonstrate that the distribution pattern of HCV genotypes has not changed much. The most prevalent HCV genotype is 1b. The subtypes 3a and 2a are present to a lesser degree and there have also been found some representatives of the genotype 1a. The increase in the detection rate of mixed infections was found to be statistically significant.