Hepatitis C virus (HCV) infects around 170 million people, 3% of the world population, and is considered a worldwide public health problem [1, 2]. The HCV genome is a 9.4 Kb single stranded RNA sequence with two untranslated regions at both ends (5 'UTR and 3' UTR) . This coding region contains a single open reading frame encoding a polyprotein of approximately 3,000 amino acids that originate at least 10 viral gene products (C, E1, E2, p7, NS2, NS3, NS4A, NS4B, NS5A, NS5B) [4, 5].
The virus represents the genus Hepacivirus of the family Flaviviridae  and it is classified into six major genotypes (1 to 6) and more than 80 subtypes. HCV genotypes may show extensive subtype diversity in some regions of the world, representing the spreading of this epidemic [7, 8]. These genotypes differ by 31 to 34% in their nucleotide sequence and by around 30% in their amino acid sequence. Accurate HCV genotyping can be used for predicting response to anti-viral therapy, as genotypes 1 and 4 are less likely than genotypes 2 and 3 to respond to interferon .
Molecular tests are essential for confirmation of persistent HCV infection and to monitor and verify the success or failure of therapy. The advantages of these tests include the possibility of early diagnosis in acute viral infection, diagnosis of infection in patients unable to mount antibody response, and confirmation of active infection . Besides its use for determining the type or duration of HCV, HCV genotyping is useful epidemiological studies, as genotypes vary among geographical regions and among different risk groups [11, 12]. Sequencing of the NS5B has been standardized and used for identification of HCV subtypes, as the region contains subtype-specific motifs, and it is also appropriate for epidemiological applications .
In Brazil, it has been estimated that around 1.5% of the Brazilian population (> 2.5 million people) is anti-HCV positive [14, 15]. Distribution of cases of chronic hepatitis C by transmission routes from 1998 to 2006 showed 21% of cases associated with intravenous drug use and 16% with blood transfusion, but in 40% of cases there was not any known risk factor . An extensive review on HCV infection data in Brazil showed the following prevalence in healthy adults and/or blood donors in the different Brazilian regions: 0.9 to 2.4% (North), 1.7 to 3.4% (Northeast), 1.0 to 1.4% (Middle West), 0.8 to 2.8% (Southeast) and 1.1 to 2.1% (South) .
Rondônia (RO) State, in North-Western Brazil, has characteristics of a highly endemic region for viral hepatitis. A study carried out with the local population in the Madeira River at Porto Velho-RO showed the prevalence of hepatitis C reached 7.4% . Ferrari et al.  investigated HCV seroprevalence among Karitiana Indians living in Rondônia and found that the HCV prevalence was 1.7%. According to the Brazilian Ministry of Health, during the period from 1999 to 2005, 1831 cases of hepatitis C were confirmed in the North Region and 400 (21.8%) of these cases were from Rondônia .
Recently, we reported the genotype distribution of HBV in Rondônia  and the present study is the first report on HCV distribution in this state. The aim of this study was to characterize the HCV genotypes circulating in Rondônia State (RO), Brazil.