A mutation described as a G-to-A transition has been reported in SDF-1 gene (SDF1-3'A), being prevalent in all ethnic groups, except in Africans. This mutation is associated with the onset of AIDS progression. Our aim was to identify the frequency of this allele in different groups from Brazil: Tiriyó and Waiampi Amerindian tribes (Asian ancestry); selected blood donors from Joinville (German descendents); and from Salvador (predominance of African and Portuguese mixture). SDF1-3'A was screened by PCR/RFLP with MspI enzyme. Our results showed a high allelic frequency in Tiriyó tribe (0.24) and Joinville population (0.21), and a frequency of 0.17 and 0.05 in the Salvador population and in the Waiampi tribe, respectively. There was no statistical difference among the allelic frequencies in the studied ethnic groups, except in the Waiampi. Due to the great genetic diversity among Brazilian population and the lack of studies on SDF1-3'A allele, our study of this allelic frequency in these different Brazilian ethnic groups could be important to identification of biomarker for therapeutic support in progression to AIDS and a molecular marker for analysis of evolutionary relationships among human populations.