Macroautophagy is a highly evolutionally conserved degradation process by which cytosolic materials (including macromolecules such as proteins and lipids) and damaged organelles are broken down to their basic components. The role of autophagy is not only the elimination of materials, but it also serves as a dynamic recycling system that produces new components and energy for cellular renovation and homeostasis. The association of autophagy with the organ physiology and pathogenesis of various disorders such as neurodegenerative diseases, cancer, infection and inflammatory bowel disease has been revealed in recent years. Autophagy also plays an essential role in cellular homeostasis in kidney and counteracts age-related stress and kidney diseases. Here, we critically review the current evidence regarding autophagy in the kidney, in particular as assessed with tissue- or cell lineage-specific autophagy-deficient mice. Better insight into the mechanisms underlying renoprotective roles of autophagy will pave the way toward novel therapies for kidney diseases.