BACKGROUND Inflammatory bowel disease (IBD)-indeterminate is a subgroup of IBD that has features of both ulcerative colitis (UC) and Crohn's disease (CD). AIMS To determine the clinical course of IBD-indeterminate in children over a 25 year period. METHODS We performed a retrospective investigation on children diagnosed with IBD. Diagnosis and disease distribution of IBD was based on clinical, radiologic, endoscopic, and histologic examinations. RESULTS Four hundred and twenty children diagnosed with IBD between 1986 and 2003 were identified from the IBD registry, 78 (22%) of whom were diagnosed with IBD-indeterminate. The mean age at diagnosis was 9.2 ± 4 years and the mean follow-up period was 4.1 ± 2 years. In 2003, 18 of 78 children (23%) were reclassified by the same physician based on the endoscopic and pathologic findings as follows: eight children with CD, five children with UC, and five children with non-IBD (eg, eosinophilic colitis). During 2011, 20 of the 60 patients who had maintained an IBD-indeterminate diagnosis were located and contacted, and detailed telephone interviews were conducted by the corresponding author. Two patients were reclassified as having CD (10%), one patient was reclassified as having eosinophilic colitis (5%), six patients remained with IBD-indeterminate (30%), and eleven patients (55%) reported a complete resolution of their symptoms. The follow-up period ranged from 10-18 years (mean 12.5 ± 3 years). Children who were reclassified as having CD were significantly younger than those who maintained an IBD-indeterminate diagnosis (6.4 ± 4 years versus11.2 ± 3 years, respectively, P = 0.05). CONCLUSION Children with IBD-indeterminate remain classified as IBD-indeterminate, or were clinically reclassified as CD or non-IBD, or became asymptomatic as they transitioned into adulthood. The need for IBD-indeterminate classification is of importance, especially when deciding on management and treatment.