Over millions of years, actively replicating retroviruses entered the human genome and through time became a stable and substantial part of the inherited genetic material. A remarkable 8% of the human genome is accounted for by endogenous retroviruses, whose biological importance has not yet been elucidated. In studying the RNA of these endogenous retroviruses in the blood of living human subjects with HIV infection, we have discovered a whole new family of these viruses that had been hidden in the centromeres of specific human chromosomes. These retroviruses have specific sequences that can elucidate their chromosome of origin. As centromeres represent the most substantial remaining frontier of human genomics, these viral sequences can provide a "bar-code" that can be used to study the role of centromeres in biology and in disease. This work also highlights the efficacy of using "reverse genomics" to understand and annotate the human genome.