SummaryBreath methane excretion is uncommon in children compared with adults. Certain intracolonic conditions, however, have been associated with enhanced methane generation. We hypothesized that encopretic and constipated children, who have abnormal colonic transit times, more likely would excrete methane than healthy children. To determine the prevalence of methane excretion among children with encopresis or simple constipation, we performed breath methane analysis on such patients and age‐, race‐, and sex‐matched control subjects. Encopretic patients (mean age, 8.3 ± 3.0 years) had daily, involuntary passage of feces and clinical evidence of constipation. Constipated patients (mean age, 7.1 ± 2.9 years) had a history of hard stools and at least one of the following symptoms: infrequent defecation, dyschezia, hematochezia, difficult stool expulsion, or abdominal pain during bowel movements. Methane excretion was present in 26 of 40 (65%) encopretic patients versus 6 of 40 (15%) control patients (P < 0.001). In contrast, 3 of 27 (11%) constipated patients were methane excreters, versus 2 of 27 (7%) controls (P = 0.4). Fourteen asymptomatic encopretic patients were retested after successful therapy; eight were methane excreters initially, but five of eight did not excrete methane after treatment. We conclude that methane is produced in a large number of children with encopresis. Treatment appears to alter metha‐nogenesis in such patients. The prevalence of methane producers among constipated children is not different from the prevalence in healthy subjects. Methanogenesis in encopretic patients may be enhanced by prolonged colonic transit time or abnormal intracolonic conditions.