Approximately 8% of our genome is made up of endogenous retroviral elements. Endogenous retrovirus is a fossil record of ancient retrovirus infection and, therefore, gives important insights into the evolutional relationship between retroviruses and their hosts. On the other hand, until recently, it has been believed that no endogenous non-retroviral viruses exist in animal genomes. We lately discovered endogenous elements homologous to the nucleoprotein of bornaviruses, a negative-strand RNA virus, in the genomes of many mammalian species, including humans. We also demonstrated that mRNA of extant mammalian bornavirus, Borna disease virus, is reverse-transcribed and integrated into the host genome DNA. These findings provided novel insights not only into the interaction between RNA viruses and their hosts, but also into the mechanism underlying the gain of novelty in mammalian genomes. In this review, we will briefly summarize our recent knowledge about endogenous bornavirus elements and also introduce some recent discoveries regarding endogenous elements of non-retroviral viruses in vertebrate genomes.