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Pediatric gastrointestinal stromal tumor is an uncommon tumor, the rarity of which has made both laboratory research studies and clinical management very difficult. As we learn more about this disorder, what is emerging is that this rare cancer is markedly different in children and adults. One of the main biological differences is that pediatric patients lack activating mutations in the oncogenes that drive tumor formation in adults. The natural history of this disease also appears to be more indolent in children than in adults. In this review, we will discuss the differences between children and adults with gastrointestinal stromal tumor and some new potential therapeutic agents.This review discusses recent advances and the rationale for several recently identified molecular targets. In addition, we discuss the formation of a clinic at the National Institutes of Health that is dedicated to the study of this rare disorder.Collaborative efforts are underway to better define the natural history and clinical course of pediatric patients with gastrointestinal stromal tumor. When combined with innovative genomic and molecular studies, these dual approaches will allow for notable advances in this field.