This review is dedicated to comparative analysis of the early stages of thymus ontogeny in fish, amphibians, and mammals. Morphological and molecular-genetic aspects of the formation of thymic stroma, colonization of this organ with T-cell progenitors, and interaction of different cell populations in the course of organogenesis are considered. Particular attention is given to the hematopoietic role of the thymus during embryogenesis and new data on the origin of T-cell progenitors. The hypothesis about the possible presence in the organ of a self-sustaining population of stem cells, formed regardless of fetal hematopoiesis areas, is discussed.