The Pyrenees Mountains rise between France and Spain. At their western end live the Basques, one of the oldest populations in Europe. All the available genetic information (gene frequencies of blood groups, serum proteins, red cell enzymes, and HLA antigens) on Pyrenean populations has been gathered and subjected to two kinds of analysis: a discrete approach, in which eight separate populations have been defined according to linguistic and geographic criteria to compute genetic distances between them; and a continuous principal components analysis on gene frequencies interpolated to a regular grid. In the first approach the Pyrenean samples have also been compared to other Western European populations. Our results show that the Basque population is most genetically differentiated with respect to other Pyrenean and Western European populations. There is a strong genetic gradient along the mountain range (i.e., in an east-west direction); thus the mountains have not acted as barriers to gene flow. A Catalan-speaking sample, the Cerdanya, is slightly detached from its neighbors and seems closer to other European populations. This genetic picture together with linguistic, paleoanthropological, and archeological data points to a Mesolithic (or older) differentiation of the Cantabrian ancestors of the Basques. Moreover, the Basque genetic features are found in the northern slope of the Pyrenees far beyond the present Basque linguistic boundaries, in accordance with the most recent hypotheses on Pyrenean historical linguistics. The genetic consequences of the arrival of the first Indo-European-speaking peoples in the Iberian Peninsula are also studied; no clear genetic trace has been left of that population movement, except perhaps for the Cerdanya, an eastern valley that affords a passage between north and south.