Background: Autoimmune diseases might be linked to changes in gut microbiota. We studied microbiota pattern in newly diagnosed Idiopathic Thrombocytopenia (N-ITP) to report possible alteration of gut microbiota in N-ITP and impact on disease course. Methods: Fifty children with N-ITP aged 2-15 years and 30 control were assessed, for 7 specific microbiota genera in stool using real time PCR within the 1st week of presentation prior to therapy. Bleeding assessment tool and CBC were done initially, followed-up regularly for 3 months. Results: Most N-ITP cases had received steroids initially when indicated, early use of intravenous immunoglobulins (IVIG) in 10% and Eltrombopag was used in 20% of cases. Three quarters (n=38) of patients showed early remission. Three strains were only detected in ITP cases and absent in control group. Bifidobacterium spp. was significantly less in patient group, but in contrast was relatively higher in patients who progressed to persistent ITP (P-ITP). Lactobacillus and Phascolarctobacterium were significantly higher in patient group and the former was significantly highest in patients who showed early remission while Eubacterium was significantly higher in patients who continued as P-ITP than those who showed early remission. Lachnospiracceae was only detected in patients who showed early remission. Bacteroides was not detected neither in patients nor control. Conclusion: Gut microbiota was different in children with N-ITP, with significant difference between those with early remission and persistent ITP which might help to predict the disease course and might have an impact on ITP treatment in future.