The products of the Cdx genes, Cdx1, Cdx2 and Cdx4, are known to play essential roles in many developmental processes including neural tube closure, axial elongation and patterning the anterior-posterior axis of the developing embryo. Cdx1 and Cdx2 are both expressed in the endoderm of the embryo and persist throughout adulthood in the intestinal epithelium, but their functions and mechanisms of action in this lineage are poorly understood, in part due to the peri-implantation lethality of Cdx2-/- mice. To circumvent this limitation, a conditional loss of function strategy was used to inactivate Cdx2 in the intestinal epithelium. These conditional mutants were also crossed to Cdx1-/- mice, which are viable and fertile, to examine potential functional compensation between these family members. The major findings of this study are that Cdx2 regulates patterning and differentiation of the small intestinal epithelium, while Cdx1 does not appear to make a contribution to either process. Furthermore, Cdx operates upstream of Notch ligand Delta-like 1 (Dll1) in endoderm and mesoderm derivatives, demonstrating that Cdx function is similar in different lineages. Finally, Cdx2 cannot fulfill the requirement for Cdx1 in regulation of its own promoter in the intestine. This is the first in vivo evidence that these two family members have context-dependent functional specificity. Altogether, this study underscores critical roles and mechanisms of action for Cdx members in the developing intestine and mesoderm.