BACKGROUND: This study was conducted to explore the prevalence of and the factors affecting constipation in elementary school students in urban and rural areas. METHODS: Study subjects were 585 grade 5 and 6 students. We conducted self-administered questionnaires during October, 2009. Outcome measure was the prevalence of constipation evaluated by the Rome III Diagnostic criteria for functional constipation. Independent variables were gender, grade, residence, mother's employment status, self-rated health status, number of family members, bowel movement habit, and health behavior (nutrition, exercise, and stress). RESULTS: The multiple logistic regression analysis showed that females, grade 5 students, those with working mothers, and those physically inactive reported having constipation significantly more often. CONCLUSIONS: Our study revealed that the female gender, increasing age, mother's employment status, and physical inactivity were risk factors for constipation in elementary school students. To improve bowel function in children, health education programs and school health promotion programs targeting healthy life habits should be implemented.