Many organisms stringently regulate the number, volume and enzymatic content of peroxisomes (and other organelles). Understanding this regulation requires knowledge of how organelles are assembled and selectively destroyed in response to metabolic cues. In the past decade, considerable progress has been achieved in the elucidation of the roles of genes involved in peroxisome biogenesis, half of which are affected in human peroxisomal disorders. The recent discovery of intermediates and genes in peroxisome turnover by selective autophagy-related processes (pexophagy) opens the door to understanding peroxisome turnover and homeostasis. In this article, we summarize advances in the characterization of genes that are necessary for the transport and delivery of selective and nonselective cargos to the lysosome or vacuole by autophagy-related processes, with emphasis on peroxisome turnover by micropexophagy.During autophagy, cargos consisting of individual proteins, bulk cytosol and/or subcellular organelles, are degraded in the lysosome (or vacuole in yeast), with ensuing recycling of the amino acid and lipid precursors. Although autophagy was thought initially to enable cells to survive nutrient starvation by degradation and recycling of dispensable cellular components, it is now recognized to be involved in a plethora of cellular responses, including the regulation of organelle number [1][2][3] Autophagy is universal to all eukaryotic cells, including yeasts, worms, insects, plants and mammals [10]. In unicellular organisms, such as yeasts, it is observed primarily under nutrient starvation conditions or during the re-adaptation of cells switched from certain environments to others. Two morphologically distinct, but mechanistically related, forms of autophagy common to uni-and multicellular eukaryotes have been described. These are macroautophagy and microautophagy (Figure 1). A third form, called chaperone-mediated autophagy, has been found only in mammalian systems and is described elsewhere [9]. Autophagy is often a degradative process but it can be either selective or nonselective with respect to cargo that is turned over. The degradation of nonselective cargo is a mechanism for recycling any excess cellular components (e.g. cytosol and/or organelles) and might be a strategy for adaptation to different environments. By contrast, cells resort to selective autophagic turnover of nonfunctional or damaged organelles, or protein aggregates, that might be too large for other proteolysis machinery, such as the proteasome.Unlike the autophagic pathways, the related cytosol-tovacuole transport (Cvt) pathway, described to date only in Saccharomyces cerevisiae, delivers a limited set of specific, Morphological steps in the cytosol-to-vacuole transport (Cvt), macroautophagy and microautophagy pathways in yeast. In microautophagy, organelles and/or cytosolic proteins are engulfed by the vacuolar membrane in a Pac-Manelike fashion and degraded in the vacuolar lumen. Macroautophagy involves the formation of large (300-900 nm)...