Cell biology and microbiology are some of the oldest areas of scientific inquiry. Despite the depth of knowledge we now have in these respective fields, much remains unclear about how microorganisms interact with host intracellular organelles. Perhaps nowhere is this statement more accurate than in the role of peroxisomes in microbial infections. Peroxisomes were one of the first organelles discovered by Christian De Duve over 50 years ago (de Duve Ann N Y Acad Sci 386:1-4, 1982). These organelles are ubiquitously found in eukaryotic cells, where they serve several well-defined functions in lipid and oxygen homeostasis (Waterham and Wanders Biochim Biophys Acta 1822:1325, 2012). This chapter will discuss the emerging evidence that indicates that in addition to their functions in cellular metabolism, peroxisomes play an important role in viral infections.