Adult height is a highly heritable trait in that multiple genes are involved. Recent genome-wide association studies have identified a novel single-nucleotide polymorphism (SNP) rs1042725 in the high mobility group-A2 gene (HMGA2) and shown it to be associated with human height in Caucasian populations. We performed a replication study to examine the associations between SNPs in HMGA2 and adult height in the Japanese population based on autopsy cases. Although we could not confirm a significant association between rs1042725 in HMGA2 and adult height, another SNP, rs7968902, in the gene achieved significance for its association in the same populations, and the effect was the same as that documented previously. These findings permit us to conclude that the SNPs in HMGA2 are common variants influencing human height across different populations. Moreover, a worldwide population study of these SNPs using 14 different populations including Asians, Africans and Caucasians demonstrated that both haplotypes and genotypes for three height-related SNPs (rs1042725, rs7968682 and rs7968902) in HMGA2 were distributed in an ethnicity-dependent manner. This information will be useful for clarifying the genetic basis of human height.