The phylogeny of the human Y chromosome as defined by unique event polymorphisms is being worked out in fine detail. The emerging picture of the geographic distribution of different branches of the evolutionary tree (haplogroups), and the possibility of genetically dating their antiquity, are important tools in the reconstruction of major peopling, population resettlement and demographic expansion events. In the last 10 000 years many such events took place, but they are so close together in time that the populations that experienced them carry Y chromosomal types which can hardly be distinguished genetically. Nevertheless, under some circumstances, one can detect departures from the model of a major dispersal of people over much of the territory, as classically claimed for the European Neolithic. The results of three studies of haplogroups relevant for Southern European populations arediscussed. These analyses seem to resolve the signal of recent post-Neolithic events from the noise of the main East-to-West Palaeolithic/early Neolithic migrations. They also confirm that, provided an appropriate level of resolution is used, patterns of diversity among chromosomes which originated outside Europe may often be recognized as the result of discontinuous processes which occurred within Europe.