The aim of this study was to evaluate the association of genes that encode gap junction forming proteins and schizophrenia. Representative genetic candidates (Panx2 and Cx36) from two families of gap junction genes were selected for analysis. According to the present findings these genes represent both functional and positional candidates for schizophrenia. The sample was comprised of 381 schizophrenic patients, and the same number of matched controls was tested in this study in order to evaluate the possible influence of the aforementioned genes on the pathogenesis of schizophrenia. Four SNPs in the case of Panx2 and two SNPs in the case of Cx36 were selected for analysis. Allele-, genotype- and haplotype-wise association did not yield statistically significant results. These data do not suggest that Panx2 or Cx36 could increase the risk of schizophrenia in the Japanese population.