The enteric nervous system (ENS), the intrinsic innervation of the gastrointestinal (GI) tract, is a vast, mesh-like network of neurons and glia embedded within the bowel wall. Through its complex circuitry and neuronal diversity, the ENS is capable of functioning autonomously but is modulated by inputs from the central nervous system (CNS). The communication between the ENS and CNS is bidirectional and, together with crosstalk of these systems with microbiota housed within the GI tract, underpins the so-called microbiota-gut-brain axis. The ENS functions as a master regulator and coordinates many of the essential functions of the body, including GI motility, sensation and secretion. It is also capable of interacting with other cells, including intestinal epithelial, neuroendocrine and immune cells, to regulate their development as well as structural and functional integrity. Disruption of these ENS interactions, especially during early life, is likely to contribute to the aetiopathogenesis of disorders of the GI tract as well as elsewhere in the body, including neurodegenerative diseases. In this article, we highlight recent advances in our understanding of the roles of the ENS, especially in its complex and reciprocal interactions that influence GI motility, sensation, intestinal epithelial integrity, immunity and neuroendocrine function, particularly focusing on the influence of the ENS in early life and early life programming.