Connection of ancient human dental calculus and molecular biology has so far brought up more questions than answers. Dental calculus is a calcified dental plaque and as such, it is mostly composed of bacteria and their products. This opens a door to the research of oral health as well as pathogens found in blood or respiratory system. The presented study shows the potential of molecular research of ancient human dental calculus in connection with health and the problems with authentication of acquired results. Several potential pathogens were detected by sequencing of 16S rDNA in Early Medieval specimens, but an even greater quantity of contaminating organisms was found. How does that change the usefulness of the applied approach? Is there a right way for the interpretation of metagenomic data derived from ancient samples?