Background: Infections with hepatitis B virus (HBV) and hepatitis C virus (HCV) can lead to chronic liver disease and hepato-cellular carcinoma (HCC). This cross-sectional study estimated the prevalence and identified risk factors associated with Hepatitis B surface antigen (HBsAg) and HCV antibody (anti-HCV) sero-positivity among children 1 to 15 years of age. Methods: The study targeted the low to middle socioeconomic population that comprises 80% to 85% of the population. Consent was obtained from parents of the eligible children before administering questionnaire and collected a blood sample for anti-HCV and HBsAg serology. Results: 3533 children were screened for HBsAg and anti-HCV. 1826 (52 %) were males. 65 (1.8 %) were positive for HBsAg, male to female ratio 38:27; mean age 10 ± 4 years. 55 (1.6 %) were positive for anti-HCV with a mean age 9 ± 4 years. 3 (0.11%) boys were positive for both HBsAg and anti-HCV. The overall infection rate was 3.3 % in the studied population. Hepatitis BsAg was more prevalent in subjects who received therapeutic injections 45 (69.2%) positive [Odd Ratio OR = 2.2; 95% Confidence interval Cl: 1.3-3.6] inspite of using new needle and syringe 44 (67.7%) positive [OR = 2.2; 95% Cl: 1.3-3.7] and vaccination in the government healthcare facilities 46 (70.7 %) positive with [OR = 3.0; 95% Cl: 1.4-6.4]. These factors were not significant in anti-HCV positive cases. Conclusion: There is a need to educate general population regarding HBV and HCV infection and risks associated with inappropriate therapeutic injections. Hepatitis B vaccine should be administered to all newborns regardless of maternal HBsAg status.