Trimethoprim-sulfamethoxazole and metronidazole were used for 14 days to treat 20 children with small intestine bacterial overgrowth (SIBO). SIBO was diagnosed using the lactulose hydrogen breath test. The breath test was repeated 1 month after treatment, and 19 (95.0%) of 20 children showed no evidence of SIBO (P < 0.001). The area under the individual curves showed that children with SIBO exhibited greater hydrogen production before treatment in both the first hour and between 60 and 180 minutes after the breath test. The treatment did not decrease methane production. In conclusion, trimethoprim-sulfamethoxazole and metronidazole was effective in treating children with SIBO.