The aim of the present study was to assess the prevalence of small intestinal bacterial overgrowth (SIBO) in multiple sclerosis (MS) patients compared with sex and age matched controls without MS. The present study was a case-control type, it included 118 patients with definitive MS and 118 age-sex matched controls. All patients and controls underwent the glucose breath test to assess SIBO.Forty-five of the 118 MS patients were SIBO positive (38.14%; 95%CI: 29.37%–46.90%) compared with 10 of 118 in the control group (8.47%; 95%CI: 3.45%–13.50%); the difference was statistically significant (P < 0.0001; OR, 4.50; 95% CI, 2.38–8.50). The data shows the mean hydrogen concentrations (ppm) obtained from the breath tests of MS with and without SIBO. Multivariate analysis showed that EDSS and MSSS score were the only factors associated with the SIBO-positive status in MS patients (OR, 3.44; 95% CI, 1.56–6.99; and OR, 2.76; 95% CI, 1.42–4.94, respectively). SIBO is highly prevalent in Chinese patients with MS. Further analytical work is required to establish a causal association between SIBO and MS risk and progression.