Hematopoetic stem cell transplantation (HSCT) is one of the main and final therapeutic protocols in patients with hematological disorders and malignancies all around the world. Use of immunosuppressive agents in HSCT recipients increases the risk of primary and or recurrent viral infections. Between viral agents, hepatitis type B virus (HBV), and hepatitis type C virus (HCV) infections have a special role in induction of acute and chronic hepatitis in transplant patients. In this research for determination of the role of HBV, HCV, and HDV infections in HSCT patients, the prevalence of different serological and molecular markers of this viruses were studied in HSCT donors and recipients. In this retrospective and cohort study the 56 recipients and 53 donors of HSCT were included. One EDTA-treated blood sample was collected from any donors and recipients pre-transplantation. Also for 3 months (one sample per-month) the blood sample were collected from HSCT patients. Antibodies and antigens of HBV, HCV, and HDV viruses included: HBs Ag, HBs Ab, HBe Ag, HBe Ab, HBc Ab (IgG&IgM), HCV Ab, and HDV-Ag and Ab were analyzed by third generation ELISA kits. The presence of HBV and HCV genomes in these samples were studied by HBV-PCR and HCV-RT-PCR, respectively. Results: HBV-DNA was diagnosed in 2% of donors, 7.5% of recipients (pre-transplantation), and also in the mean of 3.8% of HSCT patients post-transplantation. In 32% of HSCT donors, 43.4% of HSCT patients (pre-transplantation), and in the mean of 42.5% of HSCT recipients (post-transplantation), HCV genome were detected. High prevalence of HBV and HCV serological and molecular indexes and also co-infections of these viruses with together were detected in BMT patients. Significant correlations were diagnosed between these viral infections with the questionnaire data. In conclusion, for high prevalence of HBV and HCV infective markers in HSCT donors and recipient’s pre and post-transplantation, accurate detection and monitoring of these viral infections in pre and post-HSCT periods is needed.