Background: Hepatitis B virus (HBV) and Hepatitis C virus (HCV) infections are the leading causes of liver diseases causing serious health problem throughout the world. The risk of transmission of these viruses is highly associated with precutaneous exposure to blood when invasive procedures are undergoing especially in developing countries where there is improper utilization and inadequate sterilization of medical equipment. Objective: The aim of this study was to asses’ prevalence of HBV and HCV infection and its associated factors among surgical patients at Hawassa University comprehensive specialized hospital. Methods: Hospital based cross sectional study was conducted on 422 patients scheduled for surgery from January to April 2018g technique. Patients were selected by systematic random sampling .After obtaining an informed written consent and assent, structured questionnaires was used to collect data on socio-demography and associated factors. Patient’s serum was tested by serological rapid kits for hepatitis B surface antigen (HBsAg) and anti-HCV. HBsAg positive patients were further tested for hepatitis B e antigen (HBeAg). Data were analyzed by using SPSS version 20. Result: In this study, the prevalence of HBsAg and Anti- HCV among patients scheduled for surgery were 9% [95% confidence interval (CI): 6.4%-11.8%] and 5.5% [95% confidence interval (CI): 3.3% -7.6%], respectively. The rate of HBV infectivity was high with 34.2% of HBsAg positive patients having evidence of HBeAg in their serum. Patients who practiced multiple sexual partner (AOR=2.58, CI: 1.18-5.61, p=0.017), dental procedure (AOR=4.20, CI: 1.87-9.55, p=0.001) and blood transfusion (AOR=3.84, CI: 1.27-11.65, p=0.017) had higher odds of HBV infection and those who had history of surgical procedure (AOR=6.05:95%CI:1.59- 23.04:p=0.008) and dental procedure (AOR=3.70:95% CI:1.40-9.77: p=0.008) had higher odds of HCV infection, compared to their counterparts. Conclusion and Recommendation: High prevalence of Hepatitis B and C virus infection was observed among patients scheduled for surgery in the study area. This finding suggests that Health care providers in this environment have a high risk of exposure to hepatitis B and hepatitis C virus History of: dental procedure, blood transfusion and multiple sexual partners were independent risk factor for HBV infection. While, History of dental and surgical procedures were independent risk factor for HCV infection. Therefore, it is essential to routinely screen all patients undergoing surgery and Health care providers should be immunized at the beginning of their professional life and Universal biosafety measures should be observed strictly in all invasive procedures.