The prion hypothesis, once a heretical violation of the central dogma of molecular biology, has become an accepted mechanism used to explain a host of progressive neurodegenerative diseases in mammals and heritable phenotypes in yeast. From the beginning, mathematical models have been an essential tool in studying prion and other protein misfolding/aggregation processes. In this work, we review some of the major mathematical studies that have contributed to our understanding of prion disease and discuss trends in current and future studies.