Neonatal gastrointestinal (GI) mucormycosis is a rare, usually fatal, opportunistic fungal infection, which is difficult to diagnose early or preoperatively. We report three babies, only one of whom survived, with a review of the literature. All three had similar findings of necrosis of colon with multiple perforations. While the first baby was diagnosed as long segment Hirschsprung's, the second was treated as small left colon but went on to show signs of peritonitis. The third presented with pneumonia, which progressed to sepsis and peritonitis. All three were diagnosed by histology postoperatively and two of them succumbed, one in spite of amphotericin and the other as he was too sick to start antifungals and had a rapid downhill course. The one who survived did so even though she did not receive amphotericin, but had clear margins of resection. The only chance of survival in this fatal disease is early diagnosis and rapid institution of aggressive therapy inclusive of adequate surgical debridement and appropriate antifungal medications.