Background Constipation is a prevalent health disorder. There have been few epidemiological surveys on constipation in Japanese children. The aim of this study was to evaluate the prevalence of non-daily bowel movements ( BM) and irregular BM among children and to identify modifiable lifestyle factors relevant to bowel habits. Methods Subjects were from the Toyama Birth Cohort Study in Japan. A total of 7762 children aged 9-10 years were investigated via questionnaire in 1999. We evaluated bowel habit and the relationship between lifestyle and BM. Non-daily BM and totally irregular BM were defined as dependent variables in the present study. Results Non-daily BM were reported by 21.8% of boys and by 31.6% of girls, while 10.6% of boys and 18.3% of girls had totally irregular BM. Non-daily BM were significantly associated with skipping breakfast ( OR, 1.23), slow eating ( OR, 1.13), physical inactivity ( OR, 1.50) and late wake up ( OR, 1.29). Totally irregular BM were significantly correlated with skipping breakfast ( OR, 1.30), slow eating ( OR, 1.41), physical inactivity ( OR, 1.27), long TV viewing ( OR, 1.52), late bedtime ( OR, 1.43), and short sleep duration ( OR, 1.33). More girls had non-daily and totally irregular BM than boys, and these sex differences were not reduced after adjusting for lifestyle variables. Conclusions Non-daily and totally irregular BM are common in children, and there are many relevant lifestyle factors. Establishing regular lifestyle habits may lessen constipation.