A single epithelial layer serves as the interface between the organism and the contents of the gastrointestinal tract, underlining the importance of regulating cellular viability despite an onslaught of pathogens, toxins, waste by-products, and cytokines. A balance between cellular proliferation and apoptosis is necessary to maintain this critical barrier. Recent findings have begun to explain the mechanisms by which intestinal epithelial cells are able to survive in such an environment and how loss of normal regulatory processes may lead to inflammatory bowel disease (IBD) and predispose to inflammation-associated neoplasia. This review focuses on the regulation of physiological apoptosis in development and homeostasis and on pathological apoptosis in intestinal disease, inflammation, and neoplasia, identifying remaining questions and areas of needed investigation.