Cyp26a1, a gene required for retinoic acid (RA) inactivation during embryogenesis, was previously identified as a potential Tbx1 target from a microarray screen comparing wild-type and null Tbx1 mouse embryo pharyngeal arches (pa) at E9.5. Using real-time PCR and in situ hybridization analysis of Cyp26a1 and its two functionally related family members Cyp26b1 and c1, we demonstrate reduced and/or altered expression for all three genes in pharyngeal tissues of Tbx1 null embryos. Blockade of Cyp26 function in the chick embryo using R115866, a specific inhibitor of Cyp26 enzyme function, resulted in a dose-dependent phenocopy of the Tbx1 null mouse including loss of caudal pa and pharyngeal arch arteries (paa), small otic vesicles, loss of head mesenchyme and, at later stages, DiGeorge Syndrome-like heart defects, including common arterial trunk and perimembranous ventricular septal defects. Molecular markers revealed a serious disruption of pharyngeal pouch endoderm (ppe) morphogenesis and reduced staining for smooth muscle cells in paa. Expression of the RA synthesizing enzyme Raldh2 was also up-regulated and altered Hoxb1 expression indicated that RA levels are raised in R115866-treated embryos as reported for Tbx1 null mice. Down-regulation of Tbx1 itself was observed, in accordance with previous observations that RA represses Tbx1 expression. Thus, by specifically blocking the action of the Cyp26 enzymes we can recapitulate many elements of the Tbx1 mutant mouse, supporting the hypothesis that the dysregulation of RA-controlled morphogenesis contributes to the Tbx1 loss of function phenotype.