Objective: We aimed to determine MHC Class 2 allele frequencies of chronic hepatitis B cases (CHB) and inactive hepatitis B (IHB) carriers in our population, and to asses the prognosis of disease according to MHC Class 2 type in early stage. Material and Methods: Forty-eight CHB patients, 46 IHB carriers and 100 normal control subjects participiated in this study. DNAs were amplified by PCR using appropriate oligonucleotides. Then, these PCR products were displayed by agarose gel electrophoresis technique by using UV transulliminator. The polymorphism of the alleles HLA-DRB1 and HLA-DQB1 were analyzed based on genotyping including the lengths of the bands displayed on the gel. Results: The IHB carriers had significantly higher frequencies of DQB1*01, DRB1*14 and DQB1*05 alleles than the control subjects. When two groups of patients were compared, the frequencies of HLA-DQB1*01 alleles were significantly higher in the CHB patients than in the IHB carriers. The frequencies of HLA-DRB1*14-*15 and HLA-DQB1*01-*01 genotypes were significantly higher in the CHB patients than in the IHB carriers. Conclusion: It might be advised to determine HLA-DRB1*14 ve HLA-DQB1*01 aliens and HLA-DRB1*14-*15, HLA-DQB1*01-*01 genotypes in the individuals facing with hepatitis B virus, and if the results are positive, these patients should be followed up for chronicity.