Autophagy is a conserved mechanism that is essential for cell survival in starvation. Autophagy also maintains cellular health by clearing unneeded or harmful materials from cells. Autophagy proceeds by the engulfment of bulk cytosol and organelles by a cup-shaped double membrane sheet known as the phagophore. The phagophore closes upon itself to form the autophagosome, which delivers its contents to the vacuole or lysosome for degradation. Our lab is interested in how protein structures scaffold the initiation of the phagophore. A multiprotein complex consisting of the protein kinase Atg1 together with Atg13, Atg17, Atg29, and Atg31 (ULK1, ATG13, FIP200, and ATG101 in humans) has a pivotal role in the earliest steps of this process. We have solved the crystal structure of the Atg17-Atg31-Atg29 portion of the complex, and mapped the dynamic assembly pathway for the full complex. A second complex, known as the class III phosphatidylinositol 3-kinase complex I (PI3KC3-I) consists of Vps34, Vps15, Atg6, and Atg14 (VPS34, VPS15, Beclin-1, and ATG14 in mammals), and functions just downstream of the Atg1 complex. Both the Atg1 and PI3KC3-I complexes are far larger in molecular mass than would be required merely to phosphorylate their protein and lipid substrates. In this talk, I will discuss the structural organization of the autophagy initiation machinery and consider the interplay of the catalytic and possible non-catalytic functions of these complexes.