Human T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that infects human CD4(+) T lymphocytes. Despite its presence in T cells, HTLV-1 causes little overt immunosuppression. This host-virus relationship has therefore been exploited as an excellent model system for studying the dynamic interaction between a persistent retrovirus and the normal human immune system. We use a combination of mathematical and experimental techniques to identify key factors on both sides of the in vivo host-virus interaction that significantly determine HTLV-1 proviral load and disease risk. We develop a model to describe how these factors interact to enable viral persistence.