The mammalian intestinal mucosa, with its distinctive polarity, high rate of proliferation and rapid cell migration, is an excellent model system to study proliferative hierarchies and the regulation of cell division, differentiation and cell death. Each crypt contains a few lineage ancestral stem cells (the ‘ultimate stem cells’). However, there are other potential stem cells within the early lineage, and many rapidly proliferating transit cells with no stem cell capabilities. Apoptosis under two circumstances has a specificity for the ultimate stem cells in the small intestine and this represents, in one case, part of the stem cell homeostatic process and, in another case, a protective mechanism against DNA damage. Apoptosis occurs with a lower frequency in the large intestine owing to the expression of the bcl–2 gene in this region, and this probably contributes to the causes for the low cancer risk in the small bowel and the high risk in the large bowel. Current studies are beginning to unravel the complex interaction of growth factors and regulatory genes that determine whether a cell divides, differentiates or dies.