The association between squamous cell carcinoma (SCC) of the oral cavity, female genital tract, and skin with human papilloma virus (HPV) subtypes is well established in the general population and in solid organ transplant recipients, but no consistent link has been reported between HPV infection and SCC after allogeneic stem cell transplantation (allo-SCT). Studies are needed to determine if SCC, the most common secondary malignancy after allo-SCT, which is linked to chronic graft versus host disease and immunosuppressive therapy, is HPV related. Consideration should be given to assessing pretransplant HPV antibodies to identify patients at risk for HPV reactivation. If a strong relationship between HPV and second malignancies after SCT exists, studies to evaluate the immunogenicity and efficacy of quadrivalent HPV vaccine (subtypes 6, 11, 16, and 18) should be considered in both male and female long-term survivors after allo-SCT.