Autophagy is a protective mechanism that ensures cell survival. The mammalian target of rapamycin is the main regula- tor of autophagy, and mammalian target of rapamycin activation suppresses autophagy. Mammalian target of rapamycin inhibitors, like sirolimus, activate autophagy. Disorders in autophagy regulation are of central importance in many patho- physiological conditions. In the kidney, autophagy is dysregulated in autosomal dominant polycystic kidney disease, acute kidney injury, podocytopathies, transplant rejection, cold preservation ischemia, kidney aging, glomerular disease, and diabetic nephropathy. There are reasons to suspect that autophagy is dysregulated in autosomal dominant polycystic kid- ney disease. Pkd1 and 2 genes can control autophagy. There is abnormal autophagy in Pkd1 cells and polycystic kidney disease. Mammalian target of rapamycin inhibitors that activate autophagy slow cyst growth. Evidence emerging in poly- cystic kidney disease cells and polycystic kidney disease animal models shows that direct autophagy inhibition/activation affects cyst growth. The review will focus on the autophagy process, pathways that regulate autophagy, autophagy and kidney pathophysiology, and autophagy and autosomal dominant polycystic kidney disease.