We present here a quantitative way to assess the impact of language-family boundaries on population differentiation and to evaluate the homogeneity of the genetic processes along these boundaries. Our estimator (äa) of the impact of the boundary is based on an isolation by distance (IBD) model and measures the added genetic distance between populations located on different sides of the boundary. We compare this statistic with another estimator of group differentiation (FCT) computed under an analysis of variance framework that does not assume any particular spatial structure of the populations. Monte Carlo simulations are used to study the behaviour of these statistics under a two-dimensional stepping-stone model. Simulations show that FCT can suggest the existence of a frontier when populations only differ because of IBD. This spurious behaviour is much less frequent for the astatistic. However, the large variance associated with the äastatistic, and the fact that it should only be computed in the presence of IBD, may limit the use of this statistic. Overall, the origin and the effect of the boundary is best understood by comparing different statistics and by testing for the presence of IBD on each side of the boundary as well as across the boundary. We illustrate our approach by examining the boundary between Afro-Asiatic and Indo-European populations. These populations are globally genetically differentiated, but the effect of the linguistic boundary on gene flow seems geographically very heterogeneous. This boundary appears to be the result of a secondary contact between two differentiation centres rather than an enhancer of population differentiation.