The last decade has witnessed a myriad of advancements in the field of genomics, drastically changing our understanding of how genomes evolve; how genetic variation is maintained, gained, and lost; and how this variation affects gene function. In our opinion, the most relevant conceptual development has to be the renewed appreciation of the impact of genomic structural variation within species and across different species. In parallel, our newly gained ability to sequence the genomes collected from ancient populations has revolutionized how we conduct population and evolutionary genetics analyses. Combining these two exciting developments, we argue that studying the structural variation in ancient genomes will open new doors to previously unexplored areas of mammalian genome evolution. In this review, we summarize some of the recent developments in this field, most of which comes from studies in humans, and give an example where we determined the Neanderthal origins of a polymorphic gene deletion in humans combining information from modern and ancient genomes.