The serological HLA types (A, B, C and D loci) were studied in five different Indian groups in Colombia. The range of polymorphism was not very restricted in these groups, but there was significant genetic heterogeneity among the five populations in all the HLA loci. The gene frequency data, when converted into a kinship matrix and a two-dimensional eigenvector plot, showed a closer affinity between Bari and Yuko Indians, while Guane, Tunebo and Paez Indians were not only genetically different from the former but also well-differentiated from each other. It seems therefore from this study that geographical proximity may play a greater role than linguistic similarities in the genetic affinities of Colombian Amerindians.