Background: Hepatitis C virus is a hepatotropic and lymphotropic virus that has been associated with various diseases and syndromes. Autoimmune hepatitis is a chronic disease of unknown etiology, marked by the continuous inflammation of hepatocytes and necrosis and has a tendency to advance to cirrhosis. Objective: A comparative study between cases of chronic HCV infection and AIH cases regarding different parameters including their genetic association with HLA class II alleles: DRB1*01* -DRB1*15* Methodology:The study included Eighty subjects, Group I: 30 chronic HCV, Group II: 30 AIH, Group III: 20 healthy controls. HLA Typing was performed using a line probe assay. Results: HLA DRB1 * 07, DRB1 * 11 were highly associated with HCV clinical cases. DRB1*3 and DRB1*5 were the predominant alleles in AIH (representing 66.7% and 53.3% respectively). Conclusion: Certain HLA alleles of class II could be linked to hepatitis cases (either caused by HCV or autoimmune) and can predict clinical course and outcome of the disease.