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Severe sexual dysfunction and absence of sexual activity are common for long-term survivors of high-dose chemotherapy with or without total body irradiation and hematopoietic stem cell transplantation (HSCT). These treatments have known effects on gonadal function. Males and females develop abnormal hormone levels and in turn this affects sexual desire and genital organs. The sexual functioning questionnaire (SFQ), designed and tested with this population, has allowed improved understanding of the problems, quality of sexual response, and sexual behaviors in the HSCT population. Male and female HSCT survivors report more problems than age- and gender-matched healthy controls and these problems persist over time if not caught and treated early. Sexual dysfunction is a more striking problem for female survivors than males. Almost no high quality evidence supports the efficacy of interventions to treat sexual dysfunction in this population. However, promising medical and behavioral treatments are discussed for men and women.