Gastrointestinal autonomic nerve tumors form an uncommon subcategory of stromal tumors of the intestinal tract although their histologic appearance is similar to other gastrointestinal stromal tumors. Our aim was to evaluate our experience in the diagnosis and therapy of these kinds of tumors. Two patients were admitted to the Pediatric Surgery Clinic in Niš with abdominal pain and a palpable mass in the abdomen. After excision, the tumor tissue was sampled, sent for histopathological diagnosis, and examined by light microscopy, immunohistochemistry, and electron microscopy. Postoperatively, both patients recovered without complications. The patient with the tumor bulk in the mesentery of the small bowel had no evidence of tumor progression 6 years after surgery. In the second case, a giant tumor was present along the greater curvature of gaster. Even with a tumor of this size, there were no signs of progression 10 years after surgery. Radical surgical resection of gastrointestinal autonomic nerve tumors seems to be the curative approach to date, and long-term survival is possible even with large tumors.