BACKGROUND: Measuring colonic transit time (CTT) by the radio-opaque marker method is simple, widely available and important for the diagnosis of slow transit constipation. Moreover, the effects of gender and menstrual cycle on CTT remain controversial. Thus, in this study, we examined the effects of gender and menstrual cycle on CTT in healthy subjects. METHODS: We measured CTT in 42 healthy subjects (21M, 21F) by using a radio-opaque marker, Kolomark. Two simple abdominal radiographs were taken on the 4th and 7th days. Average daily intake of dietary fiber and menstrual history were surveyed. RESULTS: The mean CTT of the 42 healthy subjects was 26.5 +/- 19.4 hours. The mean CTT was not significantly different between the male and female subjects (22.3 +/- 16.1 h vs. 30.1 +/- 21.4 h, p > 0.05). However, the mean CTT of 11 female subjects in the luteal phase was significantly longer than that of 10 female subjects in the follicular phase (40.9 +/- 19.0 h vs. 20.6 +/- 19.2 h, p < 0.05). Serum progesterone level, age, BMI, and the average daily intake of dietary fiber did not correlate with CTT. CONCLUSION: The effects of the menstrual cycle should be considered in interpreting CTT in young women.