Background and Objectives: Gut microbiota is assumed to play an essential role in the pathogenesis of multiple sclerosis (MS). This study aimed to investigate the abundance of some gut microbiota among Egyptian patients with relapsing remit- ting multiple sclerosis (RR-MS). Materials and Methods: Forty cases of RR-MS diagnosed according to McDonald diagnostic criteria (2017) were recruited consecutively from the Department of Neurology, Assiut University Hospitals. The results were compared with 22 healthy age and sex matched control subjects. DNA was extracted from stool and measures made of concentration and copy number of bacterial organisms by real-time PCR using group specific primers for 16S rRNA targeting predominant genera of gut microbiota previously hypothesized to participate in MS pathogenesis. Results: The mean age was 31.4 ± 8.8 yrs; 75% of the patients were women. The mean and SD of EDSS score was 3.43 ± 1.35. Seven cases had cervical cord plaques (17%). There were significantly increased copy numbers of Desulfovibrio, Actinobacteria, Firmcutes, and Lactic acid bacteria in patients compared with the control group. In contrast there was a sig- nificantly lower level of Clostridium cluster IV in the patients. Patients who had EDSS < 3.5 had a significantly higher copy number of Actinobacteria, Bacteroidetes, and Bifidobacterium, compared with patients who had EDSS > 3.5. There was a significant negative correlation between duration of illness and copy number of Firmcutes, Akkermansia, and Lactic acid bacteria (P = 0.01, 0.04, and 0.004 respectively). Conclusion: The changes in gut microbiota are associated with exacerbation of MS disease. Disruption of the intestinal microbiota results in the depletion or enrichment of certain bacteria that may affect the immune balance leading to predis- position to MS.