We report the first study of mitochondrial DNA (mtDNA) sequencing from ancestral Amerindian populations of the South American continent. Sequencing of the D-loop region of mtDNA was carried out for bone fragments from 18 skeletons of Pre-Columbian Amerinidians. The skeletons were excavated in different archeological sites of the Brazilian Amazon region, with dating estimated at 500-4,000 years before the present. The sequencing of at least 354 bases permitted the identification of 13 haplotypes defined by variation of 26 nucleotide positions. Two haplotypes were shared by more than one sample, while 11 haplotypes were observed for a single sample. Seven haplotypes observed in 11 individuals (61% of the sample) belong to the four haplogroups described by Horai et al. (1993). Three samples that shared the transition C + T in positions 16,223 and 16,278 formed a fifth haplogroup, which has been previously described in present-day Indian populations. Finally, four samples formed a heterogeneous group but each haplotype had at least one mutation typically detected in Asian or Mongoloid populations. Thus, although only haplotypes shared by Asian populations were detected, a wide haplotype variability was observed. If our sample is representative of Pre-Columbian South America, the percentage of haplotypes (39%) not belonging to the four haplogroups described by Horai is much greater than in contemporary indigenous populations. This permits us to suggest that, in addition to the postulated bottleneck effect during the migration from Asia to the Americas, the depopulation effect started by European colonization in the 16th century contributed to the reduction in genetic variability of Amerindians.