Background Hepatitis B and C virus infection is a lead cause of morbidity and mortality among hemodialysis patients. Yet, little research has focused on the morbidity measures of these serious disorders in low and middle income countries. The study aims to estimate the prevalence of hepatitis B and C among hemodialysis patients in the West Bank hospitals in Palestine. Methods A retrospective medical records review design was performed for all governmental and private hospitals in the West Bank which provide hemodialysis services for the patients. Data was retrieved from the patients’ medical files and from the computerized health information system in some hemodialysis centers. SPSS software version 16 was used for data entry and analysis. Results In overall, 868 hemodialysis patients attending nine hemodialysis hospitals in the West Bank was recruited. The overall prevalence of hepatitis B virus was found to be 3.8 % (33 cases) with a range from 0.0 % (in Jericho and Qalqelia districts) to 11.8 % (in Bethlehem district). Regarding hepatitis C virus, the overall prevalence was estimated around 7.4 % (64 cases) with a range from 2.9 % (in Nablus district) to 15.9 % (in Qalqelia district). Conclusions Although relatively low prevalence of both hepatitis B and C virus was found in a couple of hemodialysis hospitals, some higher prevalence values urge for the implementation of stricter infection prevention measures and more effective follow up procedures.