Anomalies of the aortic arch have long been of anatomicoclinical interest. Recent studies on gene-targeted mice have identified the candidate genes that are involved in the patterning and remodeling of the pharyngeal arch arteries. In this review, we discuss our present knowledge with regard to the signaling molecules that regulate specific aspects of arch artery development. We focus first on Hoxa3, because it plays a critical role in the regulation of the differentiation of the third pharyngeal arch. Hoxa3 is expressed by the neural crest cells that originate from the rhombomeres, viz., (r)5, r6, and r7, and populate the third pharyngeal arch; it is also expressed in the third pharyngeal pouch. In Hoxa3 homozygous null mutant mice, the third arch artery degenerates bilaterally at embryonic day 11.5, resulting in the malformation of the carotid artery system. Complex combinatorial signals among the neural crest cells, pharyngeal mesoderm, ectoderm, and pouch endoderm are required for the proper development of the arch arterial system. Therefore, we highlight the numerous signaling pathways and individual genes expressed by the ectomesenchymal neural crest cells and also by the other epithelial and mesodermal cells of the pharynx. Defects in these genes result in malformations of the arch artery derivatives. This review should deepen our understanding of congenital human syndromes with abnormal patterns of pharyngeal arch arteries.