Abstract: Objective　To investigate the clinical characteristics of neonatal inflammatory bowel disease (IBD). Methods　The clinical data of two neonates diagnosed with IBD. Clinical manifestation, laboratory examination, imaging, endoscopy and histopathological findings, treatment plan and prognosis were included. Results　The clinical manifestations were fever, diarrhea, oral ulcer in two cases of neonatal IBD in this study. Laboratory findings showed inflammatory indicators (such as white blood cells, C-reactive protein) increased mainly accompanied by decreased hemoglobin, platelet, plasma albumin and other indicators. Endoscopic and pathological manifestations were significantly different in ulcerative colitis (UC) and Crohn disease (CD) children. The lesions range of UC patients were mainly sigmoid colon, and CD patients ileocecal. Conclusions For neonates with highly suspected IBD,  positive endoscopy and gene detection are recommended. Early diagnosis and standard treatment are important. For children with refractory IBD with IL-10 and IL-10 receptor gene mutations, hematopoietic stem cell transplantation is feasible and could improve its prognosis.