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Objective To investigate the clinical characteristics of glycogen storage disease typeⅠb(GSDⅠb) with Crohn's Disease(CD) and to improve the recognition of the disease. Methods Retrospectively analyze the clinical characteristics of 2 cases diagnosed with the GSDⅠb and CD in the pediatric department of Peking Union Medical College Hospital. Results A boy and a girl were included in the study. They were genetically diagnosed as GSDⅠb at 2 years age. Gastrointestinal symptoms including abdominal pain and diarrhea were observed at 4, 5 years old respectively. They were diagnosed as CD with endoscopic characteristics and pathology results. Besides corn starch, granulocyte colony-stimulating factor(G-CSF) was used to elevate the neutrophil to above 1.0×109/L. The gastrointestinal symptoms got alleviated. 5-aminosalicylic acid agents were used as supportive treatment. Conclusions Evaluation of the gastrointestinal system is necessary as the abdominal pain or diarrhea were observed in GSDⅠb patients. G-CSF with a relatively low dose is the mainstay to elevate neutrophil with few side effects. Splenomegaly is the most common side effect. Monitor renal function is necessary in the use of 5-ASA.