The mouse Cdx1 gene encodes a homeobox-containing transcription factor and is one of the few homeobox genes known to be expressed in endodermally derived tissues of the intestine in fetal and adult mice. A detailed and systematic study of the expression of the Cdx1 protein was carried out during embryonic intestinal development, postnatal cytodifferentiation and in the regenerating (after radiation-induced damage) intestine of the mouse. Using antibodies directed against Cdx1, we show for the first time that the Cdx1 protein is localised in the proliferating immature epithelium during intestinal development. It becomes restricted to the proliferative crypt compartment during postnatal differentiation, as well as in the adult intestine. The mesenchymal layer was completely negative both during embryonic development and in the postnatal intestine. The expression of the protein was first clearly detected throughout the simple columnar epithelium at day 15 of development. This expression progressively became restricted to the regions of epithelial proliferation in the crypts of the adult mouse by day 40 of post-natal development. There were occasional cells that were Cdx1 positive in the villi. During regeneration of the epithelium after radiation-induced damage, Cdx1 expression diminished during the initial phase of cellular regression. The expression was then very strong in the regenerating epithelial foci, but not in the quiescent sterilised crypts between day 4 and 6. The normal pattern was restored between day 6 and 7. The Paneth cells were negative. The physical segregation of Cdx1 with the proliferative compartment and the hierarchy of cell renewal in the intestinal epithelium is an important example of how regulatory genes function in the maintenance and in the dysfunction of renewing tissues.