BACKGROUND: HBV infection annually accounts for 1 million deaths worldwide as a result of cirrhosis, liver failure, and hepatocellular carcinoma. In addition to varying responses to antiviral therapy, HBV genotypes have also been shown to be associated with different pattern of disease progression. Despite a high HBV prevalence of >8%, very few studies have been carried out in Cameroon to determine the genotype distribution across the country. The aim of this study was to determine the prevalent genotypes, level of viraemia and correlate these parameters with liver enzymes known to be the most affordable and widely used biomarkers for monitoring disease progression in Cameroon. METHODS: This was a hospital-community based study in which 81 participants who had been previously diagnosed of HBV were recruited and screened for HIV, HCV (for exclusion) and HBsAg for confirmation. Fifty known negative cases for HIV, HBV and HCV were tested and recruited to be used as healthy controls. Viral load and genotyping was performed only for HBV-mono infected cases using the Abbott RealTime HBV automated m2000 system and INNO-LiPA HBV Genotyping assay respectively. Liver enzymes were measured by spectrophotometry on both hepatitis B positive and healthy control cases. RESULTS: The mean alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were significantly higher (p < 0.001) in HBV infected patients than "healthy controls". Of the 81 HBV infected cases viral load was detected in 76 (93.8%) with mean viral load of 120,807 IU/ml ± 440,159 SD. Mean viral load was significantly different in patients with abnormal AST and ALT when compared with patients who had normal ALT and AST. The identified genotypes in order of prevalence were A (47.4%), E (39.5%), C/E (3.9%) A/C (2.6%), A/E (2.6%), B (1.3%), A/B (1.3%) and B/C (1.3%). CONCLUSION: Genotype E was significantly associated with higher mean viral load and mean AST levels. However, aminotransferase levels may not be a good marker for HBV disease progression as some patients could have normal levels but still present with very high viral loads and therefore, remain active HBV infection with possible high transmission.