Autophagy is a lysosomal degradation pathway. Numerous human diseases, such as cancer, and infectious and developmental diseases have been linked to aberrant autophagy. Besides its disease relevance, autophagy is a unique system for investigating the basic principles of organellar biogenesis because, unlike many organelles that are rich in membrane and protein components (endoplasmic reticulum, mitochondria, etc), autophagosomes are relatively simple. Autophagosomal biogenesis responds to a variety of internal and external signals, making fine genetic or chemical manipulation possible for understanding molecular mechanisms and defining new targets for disease treatment. Canonically, nascent autophagosomes fuse with lysosomes to deliver their cargos for degradation. However, under certain circumstances, autophagosomes appear to also have degradation-independent functions, for example, protein secretion. We propose that the canonical and non-canonical roles of autophagosomes co-operate to guide cells through critical stages of development, such as meiosis, when the cell is programmed to undergo drastic cellular content degradation and structural remodeling. Our studies will shed light directly on autophagy functions in eukaryotic gametogenesis, the production of sperm (spermatogenesis) and oocytes (oogenesis), and more broadly, on how the autophagic machinery rearranges membranes for crucial aspects of development.