The analytical point of departure in this paper is the ongoing debate, initiated by Ulrich Beck, on methodological nationalism within the social sciences. Based on a comprehensive study of research collaboration and mobility of researchers this paper discusses possible traces of methodological nationalism in comparative studies of research performance. These studies are often carried out as country comparisons with no or little focus on the growing transnationality of what is measured. However, research is a transnational activity and must be understood as such. Researchers increasingly collaborate with researchers in other countries. The national research institutions are increasingly transnationalised due to the growing mobility of researchers. Based on an examination of all the papers registered in the Thompson Reuter’s Web of Science database we follow the development in research collaboration in the period 1980–2014 for 17 leading research countries.