Knowledge of the embryogenesis of the pharyngeal apparatus is the only means of understanding the “architecture” of the neck. The embryonic pharynx (which includes future oral and nasal cavities) is a much more extensive area than the adult pharynx. The main feature of the developing pharynx is a series of arches, internal pouches, and external clefts, which together comprise the pharyngeal apparatus. This structure is associated with other developing splanchna of the neck, e.g., the thyroid and parathyroid glands, tonsils, and thymus. Within each of the pharyngeal arches are the developing aortic arches and, specific for each arch, cranial nerves. The complex relations of the mesenchymal derivatives of arches (muscles, cartilage, bones) with the neurovascular bundles within each arch are presented and explained. The pharyngeal apparatus undergoes dramatic transformations: pouches and clefts disappear without interruption (interruption would produce gills and support the misnomer “branchial apparatus”). In addition, in the lateroventral neck, somites migrate to produce other muscles such as sternocleidomastoid and trapezius innervated by spinal nerves. Lateral congenital anomalies largely rely on persistence of a cleft/and or pouch or communication between the two. Their tracts have a “crooked” course among other entities generated by alterations that take place during embryogenesis.