Sexual dysfunction is a common long-term complication of hematopoietic stem cell transplantation (HSCT). We assessed the extent to which HSCT survivors and their partners agree on the importance of and satisfaction with sexual activity and causes of sexual dysfunction, using a cross-sectional survey. Ratings of the importance of sexual activity were significantly higher in survivors than those of partners (2.57 vs. 2.14, P < 0.01). More survivors (48.4%) tried to discuss about sexuality with their partners than partners themselves (23.1%, P < 0.01). Male survivors were more likely to be sexually active than female survivors (odds ratio [OR] 5.04, 95% CI 1.85, 13.74). While 23.3 and 38% of male survivors and partners reported "rejection of partners" as a cause of sexual dysfunction, only 13.3% and none of female partners and survivors pointed this as a cause of sexual dysfunction respectively. There was poor concordance between survivors and partners in attitudes toward sexuality, satisfaction with sexual activity, and causes of sexual dysfunction. Couples who considered adequate sexual activity important were more likely to be sexually active than those who did not (OR 5.53, 95% CI 1.18, 25.89). Our study highlights the need for providing information and counselling about sexuality both to survivors and partners.