Beta thalassemia minor (BTM) is a hereditary disease caused by defective globin synthesis and it is frequently asymptomatic or only mildly anemic. Female sexual dysfunction affects 21-41% of women worldwide. In this study we aimed to investigate female sexual dysfunction in subjects with BTM. A total of 183 subjects who had regular sexual intercourse with marital partners were enrolled in this cross-sectional study. The study group was comprised of 87 subjects with BTM and the control group included 96 healthy subjects. Hemoglobin electrophoresis were performed in all subjects, and all participants were assessed by the Female Sexual Function Index (FSFI) questionnaire and the Arizona Sexual Experience Scale (ASEX). The FSFI scores of the study group were significantly lower than in the control group (19.1 ± 9.6 vs. 25.2 ± 6.6, p < 0.001). Conversely, the ASEX scores of the study group were higher than in the control group (15.2 ± 41 vs. 13.5 ± 6.1, p = 0.0085). Sexual functions were poor in subjects with BTM in this study and we conclude that certain metabolic diseases associated with BTM, such as insulin resistance, hyperglycemia and dyslipidemia, may be the main causes of sexual dysfunctions in these subjects.