Recent research has suggested a link between multiple sclerosis and the gut microbiota. 14 This prospective pilot study aimed to investigate the composition of gut microbiota in MS patients, 15 the presence of Clostridium perfringens epsilon toxin in the serum of MS patients as well as the influ-16 ence of disease modifying drugs (DMD) on epsilon toxin levels and on the microbiota. Epsilon toxin 17 levels in blood were investigated by two methods, a qualitative ELISA and by a highly sensitive 18 quantitative ELISA. Neither epsilon toxin nor antibodies against it were detected in the analyzed 19 serum samples. 16S ribosomal RNA sequencing was applied to obtain insights in the composition 20 of the gut microbiota of MS patients. No significant differences in the quantity, diversity, and the 21 relative abundance of the fecal microbiota were observed in the gut microbiota of MS patients re-22 ceiving various DMDs including teriflunomide, natalizumab, ocrelizumab, and fingolimod or no 23 therapy. The present study did not provide evidence supporting the hypothesis of a causal relation-24 ship between Clostridium perfringens epsilon toxin and multiple sclerosis.