Women with endometriosis are frequently misdiagnosed with irritable bowel syndrome (IBS) for some time before a correct diagnosis is made. Visceral hypersensitivity is a key feature in both conditions. To determine if there are distinct symptom patterns in women with IBS and endometriosis, and to determine the response of these women to a low FODMAP diet in comparison to those with IBS alone. A retrospective analysis of prospectively collected data from women attending a specialist IBS service in Christchurch New Zealand. Data from those who met Rome III criteria for IBS were sorted into two groups: concurrent endometriosis and those with IBS alone. Demographics and symptom patterns were identified from a prospective questionnaire. A low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet was taught to all women as the primary therapeutic intervention. Responses to the diet were noted against their ultimate disposition. Of the 160 women who met Rome III criteria for IBS, 36% had concurrent endometriosis. The presence of dyspareunia (P>0.0001), referred pain (P=0.005), bowel symptoms exacerbated by menstruation (P=0.0004) and a family history of endometriosis (P=0.0003) were associated with concurrent endometriosis. Seventy two percent of these women reported a >50% improvement in bowel symptoms after four weeks of a low FODMAP diet compared with 49% in those with no known endometriosis (P=0.001, odds ratio 3.11, 95% CI, 1.5-6.2). Women with concurrent endometriosis and IBS report a unique symptom phenotype. The low FODMAP diet appears effective in women with gut symptoms and endometriosis.