We screened a total of 841 Y chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). The Alu element was found in 77 cases. We tested five biallelic and eight polyallelic markers in 70 out of the 77 YAP+ chromosomes. We could identify the existence of a hierarchical and chronological structuring of ancestral and derived YAP+ lineages giving rise to four haplogroups, 14 subhaplogroups and 60 haplotypes. Moreover, we propose a monophyletic origin for each one of the YAP+ lineages. Out-of-Africa and out_of-Asia models have been suggested to explain the origin and evolution of ancestral and derived YAP+ elements. We analyse the evidence supporting these two hypotheses and we conclude that the information available supports better the out-of-Africa model