Viral Hepatitis like hepatitis B and hepatitis C are the serious cause of mortality in Pakistan. Present study estimated the prevalence and risk factors associated with Hepatitis B and C among school going children from urban and rural areas. In urban areas overall prevalence of HBV was 5% where the highest prevalence of HBV was 80% and 20% in males and females respectively while HCV overall prevalence in that area was 2% where highest prevalence of HCV was 0% in male and 100% in female. In rural areas overall prevalence of HBV was 10% where the highest prevalence of HBV was 80% in males as compared to female with prevalence of 20%, overall prevalence of HCV in that area was 8% and it was 80% in males and 75% in females. Prevalence of HBV was 60%, 20% and 20% while the HCV was 0%, 0% and 100% in age groups of 5-10, 11-15 and 16-20 years respectively in urban areas. In same age group this prevalence of HBV was 30%, 20% and 50% while HCV was 25%, 25% and 50% respectively in rural areas. Epidemiological risk factors for HBV and HCV in urban and rural areas were economic status, injection user, ear/nose piercing, hospitalization, surgery, blood transfusion and family history. Among these factors in urban areas highest HBV was 40% in poor and middle economic status, 0% in surgery, while highest HCV was 100 in poor and 0% in surgery. In rural area highest HBV was 80% in poor and 0% in surgery while highest HCV was 62.5% in poor and 0% in surgery.