This study analyses the changing effect of physical distance and territorial borders (regional, national, language) on the intensity of research collaboration across European regions. Using data on all co-publications between 313 regions in 33 European countries for the period 2000–2007, we find that the bias to collaborate with physically proximate partners did not decrease, while the bias towards collaboration within territorial borders did decrease over time. Our results show that the ongoing process of European integration is removing territorial borders, but does not render collaboration less sensitive to physical distance. Given this general trend, there is considerable heterogeneity between regions and countries in their propensity to collaborate which we attribute to differences in size, quality and accessibility. The findings and conclusions are framed within the context of European research policies.