Eukaryotic cells have to regulate peroxisomal metabolism to meet their environmental or developmental requirements. Therefore, the control of peroxisome number, which is mediated not only by proliferation but also by degradation, is an important cellular event. Here we briefly review studies on the autophagic degradation of peroxisomes, a process now termed pexophagy. Recent advances in molecular analyses of both nonselective and selective autophagic pathways have revealed a category of autophagy-related genes (ATG), many of which are shared in different pathways. In this review we introduce the functions of the shared ATG products, along with their interactions with peroxisomal factors. Physiological functions of this process (especially cellular remodeling) in mammalian cells and in a phytopathogenic fungus are also introduced.