Objectives To assess the prevalence of small intestinal bacterial overgrowth (SIBO) and methane production in children with encopresis. Study design Radiographic fecal impaction (FI) scores were assessed in children with secondary, retentive encopresis and compared with the breath test results. Breath tests with hypoosmotic lactulose solution were performed in both the study patients (n = 50) and gastrointestinal control subjects (n = 39) groups. Results The FI scores were significantly higher in the patients with encopresis who were methane producers ( P < .01). SIBO was diagnosed in 21 of 50 (42%) patients with encopresis and 9 of 39 (23%) of control subjects ( P = .06). Methane was produced in 56% of the patients with encopresis versus 23.1% of the control subjects in the gastrointestinal group ( P < .01). Fasting methane level was elevated in 48% versus 10.3 %, respectively ( P < .01). Conclusions Children with FI and encopresis had a higher prevalence of SIBO, elevated basal methane levels, and higher methane production. Methane production was associated with more severe colonic impaction. Further study is needed to determine whether methane production is a primary or secondary factor in the pathogenesis of SIBO and encopresis.