During oogenesis, the oocyte stores a large amount of maternally provided products, including mRNAs and proteins. However, after fertilization, these products are rapidly degraded and new materials are synthesized from the zygotic genome. This oocyte-to-embryo transition, also known as the maternal-to-zygotic transition, is conserved in many species and plays a pivotal role in development, because non-degraded products can hamper further embryonic development. Given that the time of early embryonic development is so rapid, ubiquitin/proteasome-mediated turnover of individual proteins is probably not sufficient to remove maternal products during the oocyte-to-embryo transition. Autophagy is an evolutionally conserved degradation system in which portions of the cytoplasm sequestered by double membrane structures called autophagosomes are delivered to lysosomes for degradation. The basic roles of autophagy are the generation of amino acids for energy and the maintenance of cellular quality. In addition to the fundamental functions of autophagy, the unique role of autophagy in removing random cytoplasmic contents including mitochondria, peroxisomes, and even lipids, may contribute to extensive cellular remodeling during the oocyte-to-embryo transition. Here we briefly review the history and molecular mechanisms of autophagy, and discuss the function of autophagy in early mammalian embryogenesis.