The human virome is composed by the set of all viruses, eukaryotic and prokaryotic, present in the human body; as each body compartment constitutes a different microenvironment, the virome varies with the body part. Additionally, other factors influence the virome composition, such as age, diet, and the presence of other components of the microbiome. The study of the virome takes advantage of the development of next generation sequencing, and has allowed the discovery of novel viruses, and the characterization of the virome in healthy and diseased individuals, allowing the association of viruses with specific diseases. Perhaps the most interesting development of the study of the virome is the interplay that viruses can have with other components of the microbiome, specifically bacteria, that can either up- or down-regulate the antiviral immune response and can therefore modulate viral infectivity. This relationship is reciprocal since viruses can in turn modulate bacterial infections. The complex interactions of the virome with other members of the microbiome in the context of host genetics, and their influence in the health status of the patient have just begun to be investigated and are not completely understood, but the findings so far indicate that the regulation of the immune response by viruses and other members of the microbiome can affect the outcome of infections.