Author Summary Approximately half of the human genome is composed of repetitive elements. Yet we do not completely understand why certain elements insert in particular genomic locations, and what determines which elements are retained and which are eliminated from the genome. To address these questions we studied endogenous retroviruses, one type of repetitive elements which occupy ~10% of the human and mouse genomes, together with genomic features characterizing various biological processes (e.g., recombination and transcription) in the neighborhoods of these elements. Using statistical techniques, we identified enrichment of genomic features in the vicinity of endogenous retroviruses of different evolutionary ages. Features overrepresented adjacent to young endogenous retroviruses are expected to have facilitated their insertion in the genome. Features overrepresented adjacent to older endogenous retroviruses are expected to have facilitated both their insertion and their chances of being sustained in the genome. Our analyses allowed us to explain the uneven distribution of endogenous retroviruses along the genome, and thus to better understand the interaction of different biological processes in shaping the evolution of genome architecture.