Background: Aplasia of the uterus and upper two-thirds of the vagina due to Mayer–Rokitansky–Kuster–Hauser syndrome prevents normal coitus which may lead to anxiety and other psychiatric problems in these women. Vaginal reconstruction improves the patients’ quality of life. This study intends to compare sexual function in normal women and women having undergone vaginoplasty for Mayer–Rokitansky–Kuster–Hauser syndrome. Methods: This descriptive and analytical study was carried out in the gynecologic clinic of Imam Khomeini Hospital in 2004 to 2008. Nineteen female patients with Mayer–Rokitansky–Kuster–Hauser syndrome and a history of vaginoplasty were compared to 30 women without any anatomical malformations in their genitalia. The female sexual function index (FSFI) was used to evaluate the problem in the two groups. The calculated scores of the two groups were compared and statistically analyzed. Results: The mean age of the patients was 29.57 (SD = 6.11) years. The mean score for sexual desire in individuals with a history of vaginoplasty was 22.84 (SD = 2.5) compared to 24.63 (SD = 2.94) in the healthy women (p = 0.033) and the mean score for sexual arousal in women having undergone vaginoplasty was 13.89 (SD = 2.47) compared to 15.27 (SD = 3.41) in the healthy individuals. Sexual arousal, orgasm and pain were not different between the two groups. Conclusion: Sexual arousal and satisfaction were not different in women having undergone vaginoplasty and women with normal sexual function. It seems that the surgery offers a better quality of life and is acceptable to women with Mayer–Rokitansky–Kuster–Hauser syndrome.