The origin of modern humans in East Asia is a hot issue in molecular anthropology. Based on results from Y chromosome, mtDNA and SNP etc, some scholars proposed that modern humans first entered East Asia by a southern route and expanded northward. However, concerning to the very diverse genetic markers of the HLA system, few analyses have been performed for East Asia. For this reason, we collected and analyzed HLA data from 76 distinct Continental East Asian populations tested for five HLA loci (HLA-A, -B, -C, -DPB1, and/or -DRB1). We observed that some HLA alleles distribute unevenly in the North and in the South, and that the genetic diversity (heterozygosity of the populations) decreased from north to south. While our results support the existence of a southern route, we also conclude that genetic contribution of ancient human migrations through a northern route has probably also been ancient and substantial.