Aberrant neuronal development is one of the integrative theories for the etiology of schizophrenia. The plexin A2 (PLXNA2) gene is one of the receptor genes for axonal guidance factors. Recently, four single nucleotide polymorphisms (SNPs), rs841865, rs752016, rs1327175 and rs2498028, from the PLXNA2 genomic interval have been reported to be associated with schizophrenia in samples from European Americans, Latin Americans and Asian Americans. We tested these four SNPs for association with disease in two Asian populations: 1140 case-control Japanese samples and 293 Chinese pedigrees (1163 samples). In the Japanese samples, significant differences in the allelic frequency and genotypic distribution of rs841865 (p=0.019 and 0.020, respectively) were observed between cases and controls. Haplotype analysis also revealed a significant association of the gene with the disease (global p=0.028). In contrast, there was no genetic contribution of PLXNA2 to Chinese schizophrenia, either by linkage analysis or association tests (allelic and haplotypic transmission disequilibrium tests). These findings suggest that PLXNA2 confers a varying genetic risk for schizophrenia among different populations.