Across all vertebrates, the anatomy of the hypothalamus and mechanisms underlying its development are highly conserved, whereas the pituitary is highly specialized structurally with considerable differences amongst classes. In birds and reptiles, the hypothalamus controls the pituitary gland through nerve impulses and the secretion of neurohormones, resulting in several hypothalamic-pituitary axes: the hypothalamic-pituitary-thyroid axis, the hypothalamic-pituitary-adrenal axis, and the hypothalamic-pituitary-gonadal axis. This article provides a foundational knowledge on the physiologic function of the hypothalamus and pituitary in birds and reptiles, and their effects on behavior, homeostasis, and disease.