Autophagy is a process of intracellular bulk degradation in which cytoplasmic components including organelles are sequestered within double-membrane vesicles that deliver the contents to the lysosome/vacuole for degradation. Autophagy has two ubiquitin-like conjugation systems, the Atg12 and LC3-II systems. In the Atg12 conjugation system, the Atg16L-Atg12-Atg5 forms 800 kDa complex that elongate autophagic isolation membrane. After completion of the formation of the autophagosome, the Atg12-Atg5-Atg16L complex dissociates from the membrane. In recent study, nonsynonymous SNP analysis has indicated that ATG16L1 is a Crohn’s disease susceptibility gene.