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As the field of ancient DNA (aDNA) enters its third decade, it is perhaps time to reflect on the amazing transformation that it has undergone. During the first two decades, analyses of aDNA were mainly focussed on mitochondrial and/or chloroplast DNA as a result of their multicopy abundance in the cell, making retrieval and reproducibility much easier. Study of mitochondrial DNA through time allows evolutionary relationships between species to be resolved, molecular clocks to be calibrated, the geographical origins of samples to be revealed, and the investigation of demographic histories. However, not until the advent of massive parallel sequencing [also know as second-generation sequencing and next-generation sequencing (NGS)] was possible to retrieve and study nuclear DNA on a more routine base. Ancient nuclear DNA can additionally be used to identify extinct phenotypes, assess the degree of admixture, and examine selection pressures. This is a short review of what has been, what may come, and how aDNA has influenced NGS. Although examples from archaeology are used to illustrate the impact of NGS technologies on the field, this approach has also been successfully applied to a range of disciplines, such as medicine and wildlife forensics.