The human polyomavirus JC virus (JCV) infects a large percentage of the population, residing in the kidneys as a long term benign infective agent (designated the archetype JC virus). A variant of JCV containing a rearranged regulatory region (designated PML-type) is known to cause the central nervous system demyelinating disease progressive multifocal leukoencephalopathy (PML), primarily in AIDS patients. Exclusion of this unstable regulatory region allows a direct comparison of both PML and non-PML (archetype) JC virus for phylogenetic analysis. Recently, a phylogenetic analysis of 22 complete genomes determined that there are at least seven different JCV genotypes and that these genotypes are supported using several methods of phylogeny reconstruction, including PGMA, neighbor-joining, and parsimony. Previous work has shown that these genotypes have evolved within specific ethnic groups. Type 1 JCV is of European origin, Types 2 and 7 are from Asia and the South Pacific, Types 3 and 6 are found in Africans and African Americans, Type 4 is found throughout the population of the United States and a single Type 5 JCV was identified in the USA. Samples have recently been collected from Papua New Guinea and Guam and preliminary evidence suggests that both samples fall near the Type 2 subtype B group, based on complete genome sequences and parsimony. It is the goal of this project to explore the number and distribution of JCV genotypes throughout the population of the world and construct a comprehensive molecular phylogeny, using UPGMA, neighbor-joining, parsimony, and maximum likelihood methods. This molecular phylogeny is a step toward better understanding the relationships between the JCV genotypes and should aid in further molecular studies of disease associated with the human JC virus. To further understand the molecular evolution of the primate polyomaviruses, an exhaustive analysis of codon usage was performed. Codon usage is usually restrained by either mutational bias or selection for translation, or a combination of both. The primate polyomaviruses BKV, JCV, and SV40 were shown to be predominantly affected by strong mutational bias toward a high A+T percentage, especially at the third codon position. However, as only two BKV strains (MM and Dunlop), three JCV genotypes (Mad-1, GS/B, and Tai-3), and one SV40 strain were investigated so far, it will be necessary to expand the number of taxa to determine overall trends in codon usage in the primate polyomaviruses.