Genetic variance of hepatitis B virus (HBV) may influence the clinical manifestation, development of hepatocellular carcinoma (HCC), and response to antiviral treatment. This was analytic cross-sectional study which aimed to investigate the distribution of HBV genotypes and subtypes among different clinical status of chronic hepatitis B in Pekanbaru. A total of fifty-two of sera from chronic hepatitis B patients in Pekanbaru was collected from March to August 2009. Statistical analysis was performed by using Fisher test. HBV genotypes were examined based on homology of S gene from this study with those of GenBank database. Of these subjects, 31 (60%) and 21 (40%) were infected by genotype C and B, respectively. Based on clinical manifestation, genotype C was predominantly found among HBsAg-positive blood donors (7/10 patients) and liver cirrhosis (7/10 patients), whereas genotype B and C were comparable among chronic hepatitis B active and hepatocellular carcinoma patients. Subtype adr (60%) was the most prevalent, followed by subtype adw (38%) and subtype ayw (2%). There were no significant difference in the distribution of HBV genotypes and subtypes among diverse clinical manifestation of HBV infection. However, genotype C was predominantly detected among cirrhotic-HCC (8/9 patients) , while genotype B was mostly identified among non cirrhotic-HCC (8/11 patients) (p=0.01). In conclusion, HBV genotype may be associated with the pathogenesis of cirrhotic and noncirrhotic-HCC
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