To present study reports the clinical characteristics, diagnosis and management of pediatric patients with inflammatory bowel disease (IBD) in China. Clinical records of 49 pediatric patients with IBD at Fudan University Children's Hospital (Shanghai, China) between July 2001 and May 2012 were reviewed. Of 49 patients (30 males and 19 females), 8 patients had ulcerative colitis (UC) and 41 patients had Crohn's disease (CD). The mean age was 10.4 years in patients with UC and 10.1 years in patients with CD. The percentages of patients with UC with abdominal pain, diarrhea or rectal bleeding were 62.5, 100 and 87.5%, respectively, and that of CD patients were 75.6, 61 and 39%, respectively. Patients with UC were underweight (37.5%), and had oral ulcers (12.5%) and arthritis (12.5%), and patients with CD were underweight (34.1%), and had oral ulcers (26.8%), anal fistulas (22%) and arthritis (19.5%). Patients with CD had a higher proportion of immunoglobulin G, C-reactive protein and erythrocyte sedimentation rate compared with patients with UC. Histologic lesions of patients with UC were primarily located in the sigmoid colon (75%), transverse colon (50%) or pan-colon (50%), and in patients with CD they were located in the distal ileum (51.2%), ileocecum (58.5%) or upper gastrointestinal tract (41.5%). All patients underwent colonoscopies and 13 underwent double-balloon enteroscopies. Standard treatment for IBD, including corticosteroids, 5-aminosalicylate, and immunosuppressants (6-mercaptopurine and azathioprine), were administered to all patients. In addition 3 patients were treated with infliximab and 10 patients were treated with thalidomide. Comprehensive assessment of clinical, laboratory, endoscopic, and pathohistological data will benefit the timely diagnosis of IBD.