It has been shown that during the luteal phase of the menstrual cycle women excrete hard stools and have delayed transit, while at the time of menses, stools are looser and more frequent. The relationship between the menstrual cycle and anorectal physiology, and whether the timing of manometry testing should be standardized within the menstrual cycle has not been previously investigated. In this study, the anorectal responses to balloon distension during days 1-4 (menses), 8-10 (follicular phase), 18-20 (luteal phase) and 24-28 (premenstrual) of the menstrual cycle in 20 healthy female volunteers (ages 18-39 years) was measured. Stools were significantly looser during menses [2.32 (2.1-2.5); mean (95% CI)] compared with the luteal phase [1.98 (1.8-2.2): F(3,30) = 3.1; P < 0.04). However, there were no changes in rectal sensitivity, distension-induced rectal motility, rectal compliance, or the volumes required to induce the initial and sustained internal aral sphincter relaxations. In conclusion, although stools become looser at the time of menses, anorectal responses to balloon distension are unaltered. This suggests that the changes in bowel habit associated with the menstrual cycle are unrelated to changes in anorectal physiology. Furthermore, routine manometric testing can be performed at any time during the menstrual cycle without fear of conflicting results.