The prevalence and type of sexual dysfunction in patients with functional gastrointestinal (GI) disorders involving the upper (functional dyspepsia) or lower GI tract (irritable bowel syndrome) were studied in 683 patients seen at a tertiary referral center and a comparison group of 247 community volunteers. Associations between sexual dysfunction and type and severity of GI symptoms, and psychological symptoms were examined. All subjects were evaluated with a validated bowel syndrome questionnaire, which included questions about sexual function. Psychological symptom severity was assessed by SCL-90R. The prevalence of self-reported sexual dysfunction in patients with functional GI disorders was 43.3% and did not differ by gender, age stratification or disease subtype: irritable bowel syndrome (IBS); non-ulcer dyspepsia (NUD), and IBS + NUD. In the comparison subjects without IBS symptoms and those with IBS symptoms but not seeking health care (IBS non-patients), the reported sexual dysfunction prevalence was significantly lower (16.1 and 24.4%, respectively, p < 0.005). Decreased sexual drive was the symptom most commonly reported by both male (36.2%) and female (28.4%) patients. Dyspareunia was reported by 16.4% of females and 4% of males with IBS, but was rarely observed in patients with NUD. Report of sexual dysfunction was positively associated with perceived GI symptom severity, but not with psychological symptom severity. Sexual dysfunction should be incorporated into the quality-of-life assessment of patients with functional GI disorders and addressed in future outcome studies.