Mitochondria are the site of oxidative phosphorylation in animal cells and a primary target of reactive oxygen species-mediated damage. To prevent the accumulation of damaged mitochondria, mammalian cells have evolved strategies for their elimination. Autophagy is one means for the controlled elimination of mitochondria; however, although there has been considerable progress in defining the requirements for nonselective autophagy, relatively little is known about the genes that regulate selective autophagy of organelles. To improve our understanding of mitochondrial autophagy in mammals, we have undertaken a genetic analysis of mitochondrial clearance in murine reticulocytes. Reticulocytes provide an ideal model to study this process, because mitochondria are rapidly cleared from reticulocytes during normal development through an autophagy-related process. Here we describe several methods for monitoring mitochondrial clearance and autophagy in reticulocytes, and show that in reticulocytes these processes require genes involved in both nonselective and selective autophagy.