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To explore the prevalence and risk factors of female sexual dysfunction (FSD) in Iran. A total of 2626 women aged 20-60 years old were interviewed by 41 female general practitioners and answered a self-administered questionnaire on several aspects of FSD including desire, arousal, pain and orgasmic disorders (OD). Criteria of sexual dysfunction followed classification by DSM-IV. The sexual function was evaluated by the Female Sexual Function Index (FSFI). The subjects were randomly identified from 28 counties of Iran. Data on medical history, toxic habits and current use of medication were also obtained. Of the women interviewed, 31.5% (759) reported FSD. The prevalence increased with age, from 26% in women aged 20-39 years to 39% in those >50 years (tested for trend P<0.001). Thirty-seven percent reported OD, 35% desire disorders (DD) and 30% arousal disorders (AD), all of which increased significantly with age. Pain disorders were reported by 26.7%, occurring most frequently in women aged 20-29 years. The educational level (P = 0.01) and marriage age (<18 years) (P = 0.04) were inversely correlated with the risk of DD, OD and AD. No significant differences were detected in smoking history (P = 0.18), the presence of previous pelvic surgery (P = 0.08) and contraception methods used (P = 0.42). A history of psychological problems (P = 0.04), married status (P = 0.03), low physical activity (P = 0.012), chronic disease (P<0.01), multiparity (P<0.05) menopause status (P≤0.01) and spousal erectile dysfunction (P = 0.01) were significantly associated with FSD. This study provides a quantitative estimate of the prevalence and the main risk factors for FSD in Iranian women.