Since its conception 33 years ago, the field of ancient DNA has rapidly evolved providing powerful molecular tools for reconstructing recent evolutionary histories of many biological species, including humans. The significant technological advancement of Next Generation Sequencing within the last 10 years has allowed for the sequencing of whole mammalian ancient genomes, granting access to thousands of times more informative markers in the nuclear genome. The gradual decline of sequencing costs along with ever improving sampling, DNA recovery and sequencing methods have made it possible to sequence hundreds of whole ancient genomes from human remains, extending the reach of ancient DNA from single genome studies into large, population-scale projects, spanning both time and geographic locality. The main aim of this thesis was to reconstruct the genetic history of the Vikings using whole genome data from a large number of ancient Viking Age individuals excavated in various sites from Scandinavia, North Atlantic, the British Isles and Eastern Europe (Chapter 2). This allowed us to address questions relating to genetic structure and relationship of different Viking groups across space and time. In addition, by analysing earlier Iron Age samples from Scandinavia and comparing the genomic data of the Vikings with other ancient datasets we could also shed light on possible demographic events that may have occurred before and during the Viking Age in Northern Europe. The diversity of human pathogens in Northern Europe was also assessed during the Viking Age, finding a wide variety of pathogenic species including prokaryotic, eukaryotic and viral species. With 378 ancient samples >0.1X average depth of coverage this is one of the largest aDNA projects conducted so far. Despite the increased genetic resolution that whole genome sequencing can offer, it unfortunately remains relatively expensive to apply for ancient human samples from temperate regions due to the poor preservation of the ancient material. In such cases, the whole mitochondrial genome sequencing can be used to reconstruct the demographic history of the human female populations. As one of my side-projects, I retrieved and analysed 52 ancient human mtDNA sequences from the South Caucasus and applied demographic modelling to assess the genetic structure of the maternal line in that region for the last eight millennia (Chapter 3). It was possible to detect a surprising level of genetic stability for the female gene pool in spite of numerous cultural shifts since the Neolithic. The extracted and sequenced DNA from ancient anthropological remains may not only contain endogenous human molecules but also pathogenic DNA, which has been extensively studied for the past few years allowing for the reconstruction of recent evolutionary histories of many pathogenic bacterial species. Most of the studies conducted so far have used human teeth and postcranial bones for pathogen detection from anthropological remains. However, in light of recent investigations suggesting that the otic capsule (petrous bone) is the best skeletal part for DNA preservation, the petrous bone gradually becomes the sample of choice in the ancient DNA community, in favour of teeth and postcranial bones. No systematic analysis has been done so far to assess the potential effect of this sample choice on the ancient pathogen retrieval in ancient samples. In the fourth chapter we evaluate the yield of pathogen DNA from the petrous bones and teeth samples using Y. pestis positive ancient samples as well as assess the overall metagenomic profile of these two skeletal parts. The results indicate that the petrous bones do not yield detectable levels of ancient plague DNA and have much lower metagenomic diversity in comparison with the teeth samples. This suggests that even though the petrous bones usually have higher levels of endogenous DNA, they are not as suitable for ancient pathogen detection to the degree that teeth are.