Since the introduction of flexible fiberoptic endoscopy in the early 1970s, esophagogastro-duodenoscopy and colonoscopy have become established procedures for the diagnosis, evaluation and treatment of gastrointestinal tract disease in the pediatric population. The development of safe fiberoptic endoscopes specially designed for neonates has allowed visualization of lesions occurring in the first days of life. Despite an increased understanding of neonatal digestive disorders deriving from this new diagnostic modality, there is little consensus on the appropriate use of endoscopic procedures in routine care of neonates. It is the feeling of the authors that widening the indications of endoscopy in the neonatal period might lead to diagnosis of discrete clinical abnormalities, which might improve the care of neonates. The techniques for performing neonatal endoscopies, the appropriate indications, the common normal and pathologic findings and the complications of these procedures are reviewed.