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The heart is the first functional organ to form during embryogenesis. Cardiac development is a multifactorial complex process requiring precise control of proliferation, differentiation, migration and survival of diverse cell types by interactive networks of genetic and environmental factors. Autophagy is a conserved catabolic pathway that degrades cytoplasmic contents in lysosomes for reutilization. It is well established that autophagy regulates the development of nervous system, osseous tissue, adipose tissue and lymphocyte. Recent evidences on the basis of in vitro cell culture systems as well as in vivo animal models suggest essential roles of autophagy in cardiogenesis. In this review, we summarize the major findings regarding emerging roles of autophagy and autophagy-related genes in cardiac development, which implicates autophagy in human congenital heart disease, the leading human birth defect worldwide.