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Abstract Background Sexual function among women undergoing hemodialysis (HD) is under-studied and there is no consensus about the effect of sexual dysfunction (SD) on their quality of life (QoL). We aimed to determine the prevalence of SD and to compare QoL between women undergoing maintenance HD with and without SD. Methods We included female end-stage renal disease (ESRD) patients undergoing HD during June 2011 in the only renal unit in the north of Ceará state, northeastern Brazil. The criteria for inclusion were age between 18 and 55, at least three months on dialysis and being sexually active. Women using antidepressant medication were excluded. We used the Female Sexual Function Index (FSFI), which evaluates six domains of sexual function, including desire, arousal, lubrication, orgasm, satisfaction and pain. The patients were classified as presenting SD if the total FSFI score was less than 26. For QoL evaluation, we used the validated Brazilian version of SF-36. This is a widely used 36-item questionnaire covering eight dimensions of QoL. Demographic data, time on dialysis, underlying etiology of ESRD, and laboratory measures were assessed in unit records. Results Of a total of 58 women, 46 (79.3%) presented SD. There were lower scores related to physical functioning (48.2 vs. 71.2; p = 0.007), bodily pain (45 vs. 67.5; p = 0.010), vitality (52.1 vs. 69.1; p = 0.026) and social functioning (57.2 vs. 76.1; p = 0.034) among women with SD compared to women without SD. Physical functioning and role-physical presented positive linear correlation with FSFI scores, respectively, r = 0.322 (p = 0.013) and r = 0.345 (p = 0.007). Conclusion The prevalence of SD among women on HD is very high, reaching nearly 80%. Women on HD with SD had worse QoL, especially physical aspects of QoL, when compared to women without SD. Therefore, approaches aiming to improve QoL among women undergoing HD should be considered.