Infantile periods may have stronger genetic influences. Recently, studies on genetic defects in the interleukin-10 (IL-10) signaling pathway have provided new insights into inflammatory bowel disease (IBD). This study is to reveal whether mutations of IL-10 signaling pathway genes contribute to the phenotypes of IBD. Forty children who were diagnosed with IBD below the age of 10 years were enrolled. We sequenced the genes interleukin-10 receptor A (IL-10RA), IL-10RB and IL-10, and analyzed the clinical characteristics of very early-onset IBD (VEO-IBD). In total, 14 out of the 40 children developed their symptoms within 1 year of age. We found mutations in IL-10RA in 7 out of the 40 children (17.5%). All seven children had developed symptoms within the first year of life. Particularly, half of the children with infantile-onset IBD had IL-10RA mutations. None of the remaining 26 children diagnosed above 1 year of age had IL-10RA mutations. No mutations were found in IL-10RB and IL-10. Identified IL-10RA mutations were p.(R101W), p.(Y91C), p.(R262C), p.(R117H) and p.(W69R). IL-10RA mutations were associated with onset of infancy (P<0.001), perianal fistulae (P<0.001), poor response to medical management (P=0.017) and early surgical interventions (P<0.001). VEO-IBD in infancy is phenotypically and genetically different disease entity from adult-onset or older child-onset IBD. It has a strong association with IL-10 receptor gene. We should consider the genotyping of genes of the IL-10 signaling pathway including IL-10RA in patients with VEO-IBD, especially in whom with onset of perianal fistulae and severe colitis.