A case of chronic granulomatous disease of childhood was first diagnosed when a 20-month-old infant developed gastric outlet obstruction. Because of the unusual clinical presentation and negative gastric mucosal biopsies, the diagnosis was delayed. A subsequent full thickness biopsy of the stomach wall which led to a correct diagnosis showed a granulomatous infiltrate in the muscularis propria. Characteristic yellow pigment-laden macrophages were seen in the gastric mucosa and pyloric lymph node. Early recognition of this chronic disorder is important not only for proper management but genetic counselling as well.