Introduction: Polycystic ovary syndrome (PCOS) affects 5-10% of reproductive-aged women. Irritable bowel syndrome (IBS) is a chronic intestinal disorder that affects up to 20% of adults, more often women. We evaluate if there is a relationship between these common conditions. Methods: Polycystic ovary syndrome and control subjects were prospectively recruited. A questionnaire was given to determine their gastrointestinal symptoms. Body mass index (BMI) and percent body fat were also calculated. Results: About 65 female subjects completed the study. Among the 36 PCOS patients, 15 subjects (42%) had IBS, compared to 3 subjects (10%) among controls (p < 0.01). Control subjects were leaner (BMI: 27.5 ± 1.1 vs. 31.4 ± 1.2 kg/m2, p < 0.05) than PCOS patients. Among women with PCOS, those with IBS had a higher BMI (32.9 ± 2.0 kg/m2) compared to those with PCOS but no IBS (30.3 ± 1.6 kg/m2) and controls (27.5 ± 1.1 kg/m2; p < 0.05). This difference was true even after correcting for BMI and age (p < 0.01). Conclusions: Women with PCOS have a higher prevalence of IBS compared to healthy controls. When IBS is present with PCOS, a higher BMI and percent body fat is seen compared to PCOS alone. © 2009 Springer Science+Business Media, LLC.