The Basque Country is inhabited by three populations: indigenous inhabitants, immigrants from other regions of the Iberian peninsula and descendants from a mixture of both groups. The principal component analysis of gene frequencies at HP, GC and PI loci shows two groups in the Basque Country: one comprising the indigenous inhabitants and those of mixed descent, the other of immigrants. The first group presents gene frequencies similar to those of inhabitants of the Pyrenees and Central Europe areas, while the second group has frequencies similar to other European and Mediterranean inhabitants.