: The pharyngeal (branchial) region represents a classic example where the relationship between ontogenesis and phylogenesis has been demonstrated. It is a region where the development of gills during ontogenesis of all chordates has been recapitulated. In the process of evolution the pharyngeal region has undergone marked changes. While it functioned to ensure blood oxygenation and regulation of a constant internal environment in aquatic animals, it had to adapt to new and more complex functions in terrestrial vertebrates. The lungs have taken on the main role of blood oxygenation and the salivary glands now regulate ionic balance. The immune organs in mammals such as the thymus and the palatine tonsil, endocrine organs such as the parathyroid glands and the parafollicular cells of the thyroid gland, which produces calcitonin (originally as independent ultimobranchial bodies), as well as a part of the ear developed from the pharyngeal region. This article briefly summarizes the current knowledge regarding the phylogenesis and development of the human thymus, parathyroids, and the thyroid gland with a focus on the influence of neural crest cells during development.