Objective: This study analyzed the relationship between methane production and colonic transit time in children with chronic constipation. Methodology: Forty children, from 3 to 13 years of age, suffering from chronic constipation were included. Methane production was defined when the breath methane concentration was greater than 3 ppm. The total and segmental colonic transit times were measured with radio-opaque markers. Results: Soiling was present in 34 (85.0 %) of 40 patients with constipation. Methane production was present in 25 of 34 (73.5 %) patients with constipation and soiling and only in 1 (16.7 %) of 6 with constipation but without soiling (P = 0.014). The medians of total colonic transit time were 80.5 and 61.0 hours, respectively (P = 0.04), in methane and nonmethane producers. Segmental colonic transit times were 17.5 and 10.5 hours, respectively (P = 0.580), in right colon, 29.5 and 10.5 hours (P = 0.001), respectively, in left colon, and 31.5 and 27.0 hours (P = 0.202), respectively, in the rectosigmoid. By the sixth week of treatment, the reduction in the total colonic transit time was greater in patients who had become nonmethane producers. Conclusion: The presence of breath methane in children with chronic constipation may suggest the possibility of prolonged colonic transit time.