In this review, the regulatory mechanisms of autophagy were described, and its interaction with apoptosis was identified. The role of autophagy in embryogenesis, tooth development, and cell differentiation were also investigated. Autophagy is regulated by various autophagy-related genes and those related to stress response. Highly active autophagy occurrences have been reported during cell differentiation before implantation after fertilization. Autophagy is involved in energy generation and supplies nutrients during early birth, essential to compensate for their deficient supply from the placenta. The contribution of autophagy during tooth development, such as the shape of the crown and root formation, ivory, and homeostasis in cells, was also observed. Genes control autophagy, and studying the role of autophagy in cell differentiation and development was useful for understanding human aging, illness, and health. In the future, the role of specific mechanisms in the development and differentiation of autophagy may increase the understanding of the pathological mechanisms of disease and development processes and is expected to reduce the treatment of various diseases by modulating the autophagic phenomenon.