Conotruncal and aortic arch anomalies represent a subclass of congenital heart disease which may share a common pathogenesis. Abnormalities of the cardiac neural crest have been implicated in these disorders, but identification of specific gene defects remains incomplete. dHAND and eHAND are two closely related basic helix-loop-helix (bHLH) transcription factors which are expressed at high levels in the developing conotruncus and aortic arches as well as other neural crest derived cell types. Mice null for the endothelin-1 (ET-1) peptide have a phenotype resembling DiGeorge syndrome with craniofacial, conotruncul, and aortic arch defects. Examination of the expression of dHAND and eHAND in the ET-1 null mice revealed that both genes were down-regulated in the pharyngeal arch which gives rise to craniofacial structures as well as in the truncus arteriosus and developing aortic arches. Cardiac muscle expression of the HAND genes was unaltered in the ET-1 null mice, suggesting that separable elements control the lateral mesodermal and neural crest components of expression of these genes. These data provide a genetic model for studying the potential interaction of multiple genes in the regulation of certain neural crest derived tissues including the cardiac outflow tract.