Abstract: Objective：To characterize the microbiome in children with IL10RA deficiency who developed inflammatory bowel disease(IBD) at a very young age. Methods：Fecal samples were collected from three groups of children. IL10RA group included very early onset inflammatory bowel disease (VEO-IBD) patients with identified IL10RA deficiency. Symptomatic patients(SP) consisted of patients that presented with signs and symptoms suggestive of VEO-IBD but without gene mutation. And healthy controls(HC) were age-matched volunteers lacking evidence of disease. Microbial DNA was extracted from the fecal samples. All analysis was based on the 16S rRNA gene sequencing data. Results：We enrolled 17 IL10RA-deficient patients, 15 symptomatic patients, and 22 age-matched healthy children. We observed significantly reduced diversity in IL10RA at both the phylum and ordinal level of taxonomic classification. The Shannon index values for HC, SP, and IL10RA group were 2.37±0.57, 1.79±0.70, and 1.36±1.03 respectively. Accordingly, average Simpson index values were 0.19±0.11, 0.32±0.20, and 0.48±0.31 respectively. A balanced proportion of genera of Firmicutes and Bifidobacterium dominant Actinobacteria were observed in HC. But in SP and IL10RA group, Firmicutes were dominant by Enterococcus and Streptococcus. Compared with SP group, the proportion of Bifidobacterium was reduced in IL10RA group, but the proportion of Rothia was increased. Seventeen genera showed significance in comparisons of relative abundances between IL10RA group and the other groups. Interestingly, most of them were negatively associated with disease status. Conclusion：Intestinal microbiome in VEO-IBD with IL10RA deficiency had features different from the other groups, such as reduced diversity, large variation of the group, imbalanced structure and decreased abundance of symbionts.