Autophagy related 16 like 1 is a protein that in humans is encoded by the ATG16L1 gene. This protein is characterized as a subunit of the autophagy-related ATG12-ATG5/ATG16 complex and is essentially important for the LC3 (ATG8) lipidation and autophagosome formation. This complex localizes to the membrane and is released just before or after autophagosome completion. Furthermore, ATG16L1 appears to have other autophagy-independent functions, e.g., intracellular membrane trafficking regulation and inflammation. Autophagy in general plays a crucial role in pathways leading to innate and adaptive immunity activation. That is why many autophagy-related proteins, including ATG16L1, their gene expression and its role in autoimmune diseases are studied in-depth nowadays. Function Autophagy is the major intracellular degradation system delivering cytoplasmic components to lysosomes, and it accounts for degradation of most long-lived proteins and some organelles. Cytoplasmic constituents, including organelles, are sequestered into double-membraned autophagosomes, which subsequently fuse with lysosomes. ATG16L1 is a component of a large protein complex essential for autophagy. Several proteins which interact with ATG16L have been identified to reveal its function. It appears that ATGL16L has an important role not only in autophagy but also in xenophagy for example during a bacterial infection, in antigen presentation in human B cells, plasma membrane repair in mouse embryonic fibroblasts, hormone secretion and in alcohol-induced sedation response in Drosophila. Structure ATG16L1 protein consists of three main domains - N-terminal region which contains an alpha-helix required for binding to ATG5 ubiquitin-folds, a middle region (coiled-coil domain, CCD), and a domain made of seven WD40 repeats, that forms a β-propeller, found in its C-terminal part. Polymorphisms and mutations in these domains are considered to be associated with several diseases. Due to present models, ATG16L1 is supposed to exist in ~800 kDa complexes which contain ATG12-ATG5 and several ATG16L1 dimers. These dimers are composed mostly of a CCD region of the protein and ATG5 binding site. The middle region is considered to be essential for the ATG16L1 function. Mice with CCD deletions exhibited phenotypic abnormalities as well as neonatal fatality, though non of these were observed in WD40 region deletion phenotype. Surprisingly, overexpression of CCD, as well as deletion, leads to an inhibition of autophagosome formation. Clinical significance ATG16L1 is expressed in the colon, intestinal cells, leukocytes and spleen. Recent studies have shown that mutations in the ATG16L1 gene may be linked to Crohn's disease. A coding polymorphism in ATG16L1 gene is considered to be