The calls of 22 populations of the Red-billed Chough (Pyrrhocorax pyrrhocorax) and the Alpine Chough (P. graculus) were sampled throughout the Palearctic region. In both species calls differed in frequencies, either by latitude or longitude in the Red-billed Chough and mostly by longitude in the Alpine Chough. Frequencies varied according to body size, being higher in smaller-bodied populations and lower in larger-bodied ones, as predicted by the inverse relationship between body size and frequency. We hypothesize that, besides the effect of physical constraints determining frequencies, past climatic events and the geomorphological history of the Pleistocene also have influenced the present pattern of diversification. We also hypothesize that gene flow and ‘cultural’ flow have constrained the evolution of clear-cut population differences between European and North African populations, whose segregation could be quite recent.