OBJECTIVE: The purpose of this study is to raise awareness of small intestinal bacterial overgrowth (SIBO) and intestinal methanogen overgrowth (IMO) prevalence among patients with endometriosis to improve global recommendations in the standard of care for endometriosis. METHODS: This case-control study included a cohort of 1027 women who underwent the lactulose breath test (LBT) during their healthcare check-up to diagnose SIBO and/or IMO from November 2021 to June 2023. One hundred and forty-eight endometriosis patients were selected based on magnetic resonance imaging or a histological assessment. Each were matched with an equal number of women without endometriosis based on the exact age. RESULTS: SIBO/IMO prevalence was significantly higher among women with endometriosis, with up to 136 out of 148 who tested positive, 91.9% (95% confidence interval [CI] 86.3-95.7%) against 123 in the control group, 83.1% [76.1-88.8%], P = 0.0223. Women with endometriosis showed a significantly higher incidence of altered transit than those without (85.8 vs. 71%, P = 0.0019) and an increased prevalence of constipation (67.8 vs. 44.7%, P = 0.0017) and dizziness (44.8 vs. 28.7%, P = 0.0245). Overall, methane overgrowth accounted for up to 63.2% in women with endometriosis who tested positive for methane overgrowth. SIBO H2 was associated with a higher risk of developing diarrhea (P = 0.0027), whereas those positive for IMO were at a higher risk of developing acid reflux (P = 0.0132). CONCLUSION: Abnormal digestive overgrowth should be assessed in all endometriosis cases, as this approach could offer a new therapeutic strategy.