The small intestinal crypt of the adult mouse represents a model system for studying cell renewal. One or more functionally equivalent stem cells located within the crypt fuel a continuous regeneration of the gut's four principal epithelial cell lineages. These lineages differentiate during a geographically well-organized migration along the crypt-villus axis. This axis does not complete its morphogenetic program until the third postnatal week. We examined the organization of the crypt-villus axis and its stem cell hierarchy in postnatal day 1 (P1) to P28 transgenic mice. These mice contained transcriptional regulatory elements from the liver fatty acid binding protein gene linked to a human growth hormone (hGH) reporter. Adult male and female animals exhibit a striped pattern of hGH accumulation in their villus-associated epithelial cells: vertical coherent bands of wholly hGH-positive epithelial cells derived from a monoclonal crypt and vertical coherent stripes of wholly hGH-negative epithelial cells derived from an adjacent crypt extend to the apical extrusion zone of their common villus. Villus striping develops in a proximal-to-distal wave that extends from the duodenum to the jejunum by P7 and to the ileum by P14. Striping occurs as a result of a loss in the ability to support transgene expression. The decision appears to affect all cells within a stripe, irrespective of their position along the basilar-to-apical axis of a villus, suggesting that it is programmed by the nascent crypt's multipotent stem cell(s). Suppression of transgene expression traverses the crypt-villus axis more rapidly than the rate of epithelial cell migration. The boundary between stripes is very sharp and does not contain cells with transitional levels of the hGH reporter, indicating that the epithelial components of the crypt-villus axis have a higher degree of organization at this stage of development than appreciated previously.