Gastrointestinal stromal tumors could rise in different areas of the digestive tract, at any age, but very rarely in neonates. We present the case of a 5-day-old male, with intestinal stenosis and atresia (type II) operated for peritonitis. On the resected specimen, the histopathological examination revealed a small gastrointestinal tumor of 8 mm. The immunohistochemical analysis indicated a low malignant potential. He is currently at two years of oncologic follow-up with no evidence of disease.