The pharyngeal arches are embryonic structures that develop into the face, neck, a part of the heart, and several endocrine glands in animals. They are thought to have played a key role in vertebrate evolution as their derivatives impact the mode of feeding and breathing. Moreover, perturbation in pharyngeal arch development is associated with several major groups of birth defects in humans. During early embryonic development, cells from all three germ layers come together to assemble the pharyngeal arches. Subsequently, the pharyngeal arches undergo growth, morphogenesis, and cell type differentiation to give rise to musculoskeletal, cardiovascular, neural, and glandular components. These processes are guided by interactions amongst different tissues, via signaling molecules. A large number of genes, with a complex network of regulatory relationships, govern each aspect of pharyngeal arch development. With the advance of molecular genetics tools in model organisms such as mice, we are beginning to understand the molecular and cellular mechanisms underlying development of the pharyngeal arches and related birth defects. This eBook will provide an introduction into development of the pharyngeal arch system, with a detailed discussion on the genetic regulation of this process.