Background/Aims: The symptoms of inflammatory bowel disease (IBD) fluctuate considerably over time. However, it has not been determined whether these symptoms are affected by the menstrual cycle in female IBD patients. This study analyzed the effects of the menstrual cycle on IBD symptom variation. Methods: This was a prospective study of 91 study subjects (47 IBD patients and 44 healthy controls) who reported daily symptoms and signs throughout their menstrual cycles. Results: IBD patients had significantly more frequent gastrointestinal symptoms, such as nausea (30% vs 7%, p=0.006), flatulence (53% vs 22%, p=0.003), and abdominal pain as compared to controls (68% vs 38%, p=0.006). The IBD patients also experienced more frequent systemic premenstrual symptoms than the controls (79% vs 50%, p=0.003). More severe abdominal pain (p=0.002) and lower mean general condition scores (p=0.001) were noted during the menstrual phase as compared to the pre- or postmenstrual phase in both groups. IBD patients experienced more frequent premenstrual gastrointestinal symptoms than controls, but their IBD symptoms did not change significantly during the menstrual cycle. Conclusions: Knowledge of the cyclic alterations in gastrointestinal and systemic symptoms may be helpful in determining the true exacerbation of disease in female IBD patients. (Gut Liver 2013; 7: 51-57).