Background: The population that inhabits the semiarid Northern zone of Chile arose from ethnic admixture between aborigines, Spanish conquerors and the influx, during the XVII century, of foreign aboriginal workers and a minority of African slaves. Aim: To study the phenotypic frequencies of 15 genetic markers among populations inhabiting valleys in the Northern zone of Chile and to estimate the percentage of indigenous, African and Caucasian admixture in these populations. Material and methods: Throughout five different field works, blood samples were obtained from 120 individuals living in the Elqui valley, 120 individuals living in the Limari valley and 85 living in the Choapa valley. Blood groups, erythrocyte enzymes, plasma proteins and HLA markers were typified. Results: In the populations studied, the contribution of non indigenous genes was low in relation with the time elapsed since the Spanish invasion. The Hardy-Weinberg disequilibrium for MNS system would have microevolutive implications. The admixture percentages in these valleys confirm ethnic and historic information. The variation of the enzyme esterase D is identical to that of other Chilean populations. Conclusions: The phenotypic and genetic frequencies in the three populations studied and different admixture of indigenous genes is inversely proportional to the geographic distance from Santiago, in Central Chile. (Rev Méd Chile 2000; 128: 593-600).