Viruses are the most abundant and diverse entities on earth. Exploration of viral diversity has traditionally been limited by the lack of common marker genes, however, the advent of viral metagenomics has made it possible to characterize global viral communities. Viruses in host-associated systems, such as human and animal tissues, are of special interest as they may be causative agents of disease. Additionally, changes in the total viral consortium may be indicative of host health status, with opportunists and pathogens replacing normal viral flora in the disease state. This dissertation presents an introduction to viral metagenomics and explores use in both human and animal associated systems. Methods in viral metagenomics, including both molecular biology and bioinformatics are reviewed as well as viral metagenomic studies to date. The metagenomic signature technique is explored as a method to characterize metagenomes and to screen for contaminating host genomic DNA sequences in viral metagenomes. Three experimental studies are presented to demonstrate the utility of metagenomics in healthy and diseased individuals. A case study of oropharyngeal viruses revealed the presence of phage-encoded virulence genes in healthy individuals, and also provided the first ever characterization of oropharyngeal viral communities. In the second study, viral communities from the airways of individuals with and without cystic fibrosis (CF) were compared. There was a striking difference in metabolic functions encoded by phage in CF versus Non-CF individuals. Regardless of which taxa were present, CF-associated phage shared a common core metabolism that reflected the disease state and aberrant airway physiology. Viral communities in healthy and diseased fish were compared in the third study. In contrast to the airway viromes, fish-associated viromes were found to differ taxonomically but not in metabolic function in the disease state. Together these studies demonstrate the power of viral metagenomics for discovery and for deciphering how viral communities change in the face of disease.