Background: Gut microbiota cluster into three enterotypes named the Bacteroides, Prevotella and Ruminococcus. While each person’s microbial “fingerprint” is unique, there are specific patterns seen in those that are healthy and those that have specific illnesses. The aim of the present study is to identify the enterotypes that are likely related to Multiple Sclerosis Egyptian patients as well as their possible role in the course of the disease. Subjects & Methods: Thirty patients with remitting relapsing multiple sclerosis, who presented to the MS Clinic of Alexandria University Hospital were enrolled in our study. These were diagnosed according to according to McDonnald 2017 criteria. A cross matching control group of 20 healthy subjects of similar age and sex were included. Stool specimens were taken from each. Quantitative SYBR Green Real-Time PCR was done for the identification and quantitation of Bacteroides, Prevotella and Ruminococcus which constitute the core of the three major enterotypes. Results: Enterotype 1 is the most common enterotype detected in MS and control cases (80% versus 65%). For Enterotype 3, it was not detected in any of the 20 control cases while detected in multiple sclerosis case (16.7%). However, by comparing the multiple sclerosis and control cases Enterotype 2 is significantly less in multiple sclerosis than control (3.3% versus 35%). Conclusion: Although Enterotype 2 is significantly less in multiple sclerosis patients, collapsing the whole microbiome variations into dominant enterotypes was not appropriate to identify disease association or to be used as a disease biomarker.