Gastrointestinal endoscopy permits direct observation of the alimentary tract, acquisition of mucosal tissue for histopathologic examination, and other diagnostic and therapeutic maneuvers. Endoscopes of appropriate size for many neonates and an expanding array of compatible tools and accessories have broadened what is possible, although few neonatal data exist to guide use. Evaluation and treatment of gastrointestinal bleeding, evaluation and dilation of fibromuscular congenital esophageal stenosis, and the bedside placement of gastrostomy tube have been described. Careful consideration of risks, benefits, and discussions between involved specialties permit patient-specific application of these tools and techniques to augment care of this vulnerable population.