Global-scale patterns of human population structure may be influenced by the rate of migration among populations that is nearly eight times higher for females than for males. This difference is attributed mainly to the widespread practice of patrilocality, in which women move into their mates' residences after marriage. Here we directly test this hypothesis by comparing global patterns of DNA sequence variation on the Y chromosome and mitochondrial DNA (mtDNA) in the same panel of 389 individuals from ten populations (four from Africa and two each from Europe, Asia and Oceania). We introduce a new strategy to assay Y-chromosome variation that identifies a high density of single-nucleotide polymorphisms, allows complete sequencing of all individuals rather than relying on predetermined markers and provides direct sequence comparisons with mtDNA. We found the overall proportion of between-group variation (Phi(ST)) to be 0.334 for the Y chromosome and 0.382 for mtDNA. Genetic differentiation between populations was similar for the Y chromosome and mtDNA at all geographic scales that we tested. Although patrilocality may be important at the local scale, patterns of genetic structure on the continental and global scales are not shaped by the higher rate of migration among females than among males.