One of the most interesting problems facing the interpretation of south central Andean prehistory is to decipher the genetic relationships among ancient groups that inhabited this region. This study evaluates the biological relationships between the ancient inhabitants of the coast and interior valleys of the Azapa region in northern Chile and the Cochabamba valleys of Bolivia, with reference to highland Tiwanaku groups. Craniometric data (N = 299) were statistically evaluated to compute group means using Mahalanobis (D²) values. Results demonstrate that there is a notable difference between coastal and interior valley populations of the Azapa region; whereas a close biological association exists between groups from the Cochabamba valleys and the interior Azapa valleys, especially for those associated with the Formative and Tiwanaku Periods.