The emergence of thermoregulation in avian species is a complex matter in which neural as well as hormonal processes are involved. In a previous paper, the neural aspects of primary avian thermoregulation were discussed. In this paper the role of the hypothalamus-pituitary-thyroid axis (HPT-axis) and the hypothalamus-pituitary-adrenal axis (HPA-axis) in the ontogeny of avian thermoregulation is evaluated. The regulatory mechanisms and different important hormones of both axes, which have stimulatory or inhibitory effects, are discussed. Because the onset of functionality of the thermo regulatory system is of great interest, the ontogeny and functionality of the hormonal axes are clarified. There is a great difference between precocial and altricial birds in hormonal events as well as in neural processes which are involved in the emergence of thermoregulation. In precocial avian species the HPT-axis becomes functional during the mid- to late embryonic period while the same axis only becomes fully functional during the first week post-hatch in altricial avian species.