Gastric perforation is a potentially fatal condition that is rare in infants and children. Most case reports in the pediatric population are of neonates or in patients with various associated risk factors including prematurity, ischemia, trauma, or ulcers. Heterotaxy syndrome is characterized by abnormal symmetry and malposition of the thoracoabdominal organs and vessels. Spontaneous gastric perforation has not previously been reported in a child with heterotaxy syndrome. We present a case of a child with heterotaxy syndrome who presented with spontaneous gastric perforation. We review the signs and the symptoms, radiographic clues, and diagnostic considerations of gastric perforation.