Autophagy is a bulk degradation system that is responsible for various cellular processes such as starvation response, cellular clearance and immune response. In this process, a double membrane structure called an autophagosome sequesters a portion of cytoplasm and delivers the contents to vacuoles/lysosomes. In yeast, at least 17 Atg proteins are shown to be essential for autophagosome formation. Here, we describe the comprehensive structural studies on Atg proteins by X-ray crystallography. Based on structural information and mutational analyses, we discuss the molecular roles of Atg proteins on autophagosome formation.