Peroxisomes are ubiquitous organelles required for many essential functions, such as fatty acid metabolism. Defects in peroxisome biogenesis cause a spectrum of human diseases known as peroxisome biogenesis disorders (PBDs). These devastating diseases lack effective therapies and it is unclear how peroxisome dysfunction causes the disease state. Animal models are needed to understand the connection between peroxisome biology and animal physiology. The fruit fly, Drosophila melanogaster, has recently become an important animal model in the study of peroxisomes. We have identified the major peroxisomal proteins and pathways in flies and examined peroxisomal protein trafficking. We have found that fruit fly peroxisomes share many features in common with higher animals, but display some important differences. Flies appear to have lost one of the pathways used in other organisms to target proteins to the peroxisomal matrix. Also some proteins are dually localized to peroxisomes and the cytoplasm likely through a weak interaction with the protein machinery that brings peroxisomal proteins into the organelle. We have also generated fly mutants with impaired peroxisome biogenesis and shown that peroxisomes are required for normal development and lipid metabolism. Flies with impaired peroxisome biogenesis also show defects in multiple processes that depend on muscle function, such as locomotion. PBD patients also display muscle defects, but it is thought to be a secondary effect of neuronal dysfunction. We propose that peroxisome loss in humans, like in flies, may directly affect muscle physiology, possibly by disrupting energy metabolism. Understanding the role of peroxisomes in fly physiology and specifically in muscle cells may reveal novel aspects of PBD etiology.