In the life sciences, where large data sets are increasingly setting the stage for research, the role of bioinformatics is expanding. This has far-reaching consequences, not only for the way research is done, but also for the way this research affects our understanding of human identity. Using two case studies of practices involving bioinformatics, the software program Structure and the Genome of the Netherlands project, I will argue that bioinformatics and its tools can be understood as ‘infrastructure’ as described by Bowker and Star. A number of value decisions are involved in the development of such tools. However, once the tools are ready for use, these values tend to blend into the background of the research. This may lead to the ‘naturalisation’ and ‘essentialisation’ of value-imbued aspects of population identities such as nationality, ethnicity and race.