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We have analyzed eight human-specific Alu insertion polymorphisms in four Chinese populations belonging to three ethnic groups (98 Hans from Shanghai, 80 Hans from Guangzhou, 85 Uyghurs, and 60 Sibos). All populations exhibited high levels of average heterozygosity, and those in Uyghur and Sibo were higher than predicted by the island model of population structure. The degree of genetic differentiation among these populations is statistically significant, and lower than those observed in most parts of the world except for Europe and Sahul (Australia and New Guinea). Phylogenetic analysis of these data with published data from 29 worldwide populations shows that there is a close genetic affinity among all the East Asian populations except for the Uyghur, and that the Uyghur population was found to lie between the East Asian and the West Asian populations on the population tree. The greater heterozygosity and the significant genotype associations between unlinked loci observed for the Uyghurs support the scenario that the Uyghurs might have originated from an admixture between Europeans and East Asians. This study also provides further support for the “out-of-Africa” hypothesis of modern human evolution in East Asia.