We defined the Y-chromosome haplotypes on the basis of six polymorphic sites: an Alu-element insertion (YAP), a single-base change (C→T at DYS199), one trinucleotide repeat (DYS392) and three tetranucleotide repeats (DYS393, DYS390 and DYS19). Among 140 Y chromosomes from Whites, Blacks, Japanese and Amerindians we identified 67 different haplotypes, the majority of them population-specific; only seven haplotypes were shared by three different racial groups, mostly owing to admixture. Overall, three main lineages can be defined on the basis of the YAP/DYS199/DYS392 markers: (a) a predominant /−/C/10/13/22 (or) 23/ lineage, observed among all racial groups; (b) a/+/C/ lineage which predominates among Blacks (comprising mainly the sublineage /+/C/10/13/), although it is eventually found among Japanese and Whites; and (c) a /−/T/ lineage observed only among Amerindians (comprising mainly the sublineage /−/T/13/13/). The decreasing haplotype diversity of the three lineages agrees with the idea that the first is the most ancient, while the last is the more recent. The data also indicate that the YAP insertion occurred in a /−/C/10/13/ chromosome and the C→T mutation occurred in a /−/C/13/13/ chromosome. Finally, the data suggest that at least two Y-chromosome lineages (/−/C/13/ and /−/T/13/) contributed to the early peopling of the Americas, and supports the hypothesis that /−/T/13/ could be derived from /−/C/13/ and that both haplotypes could be present in the ancestral populations that peopled the continent.