The CYP2C9 gene have three common alleles, CYP2C9∗1, CYP2C9∗2 and CYP2C9∗3, associated with different homozygous (∗1/∗1, ∗2/∗2 and ∗3/∗3) and heterozygous (∗1/∗2 and ∗1/∗3) genotypes, which in turn are related to extensive (gEM), intermediate (gIM) and poor (gPM) metabolizers. Likewise, the inter-ethnic variability was intimately associated with different drug metabolism. Therefore, the aim of the present study was predict the metabolizer phenotypes in different Peruvian ethnic groups from lowland (<2,500 m) and highland (>2,500 m). TaqMan genotyping assays were performed in a group of 174 healthy unrelated Peruvian individuals. In this study, the allelic comparison between the three eco-regions showed that the CYP2C9∗1 was the most common in Andean (96.32%); the ∗2 was the most frequent in Coast (7.45%, p<0.05). Regarding the ∗3 was the most common in Amazonian (6.25%, p<0.05). In a corroborative manner, the gEM was the most common in Andean (94.74%), the gIM in Coast (17.02%) and gPM in Amazonian (6.25%) populations. Our study provides a valuable source of information about to metabolizer phenotype drugs in different Peruvian ethnic groups. In this way, it could be established suitable genetic-dosage medicaments for various common diseases in these heterogenetic populations.