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Ancient demographic events can be inferred from the distribution of pairwise sequence differences (or mismatches) among individuals. We analyzed a database of 3,677 Y chromosomes typed for 11 biallelic markers in 48 human populations from Europe and the Mediterranean area. Contrary to what is observed in the analysis of mitochondrial polymorphisms, Tajimäs test was insignificant for most Y-chromosome samples, and in 47 populations the mismatch distributions had multiple peaks. Taken at face value, these results would suggest either (1) that the size of the male population stayed essentially constant over time, while the female population size increased, or (2) that different selective regimes have shaped mitochondrial and Y-chromosome diversity, leading to an excess of rare alleles only in the mitochondrial genome. An alternative explanation would be that the 11 variable sites of the Y chromosome do not provide sufficient statistical power, so a comparison with mitochondrial data (where more than 200 variable sites are studied in Europe) is impossible at present. To discriminate between these possibilities, we repeatedly analyzed a European mitochondrial database, each time considering only 11 variable sites, and we estimated mismatch distributions in stable and growing populations, generated by simulating coalescent processes. Along with theoretical considerations, these tests suggest that the difference between the mismatch distributions inferred from mitochondrial and Y-chromosome data are not a statistical artifact. Therefore, the observed mismatch distributions appear to reflect different underlying demographic histories and/or selective pressures for maternally and paternally transmitted loci.