There is a growing body of evidence that the spread of farming in Europe was not a single uniform process, but that it involved a complex set of processes such as demic diffusion, folk migration, frontier mobility, and leapfrog colonisation. Archaeogenetic studies, which examine contemporary geographical variations in the frequencies of various genetic markers have not succeeded in addressing the complex Neolithisation process at the required level of spatial and temporal resolution. Moreover, these studies are based on modern populations, and their interpretive genetic maps are often affected by post-Neolithic dispersals, migrations, and population movements in Eurasia. Craniometric studies may provide a solid link between the archaeological analysis of past events and their complex relationship to changes and fluctuations in corresponding morphological and thus biological variations. This paper focuses on the study of craniometric variations between and within Pre-Pottery Neolithic, Pottery Neolithic, and Early Neolithic specimens from the Near East, Anatolia and Europe. It addresses the meaning of the observed multivariate morphometric variations in the context of the spread of farming in Europe.