Background:Schizophrenia is a relatively common disorder, with a lifetime prevalence of about 1%. Family history is the most important risk factor for schizophrenia, consistent with a genetic contribution to its etiology. Recent human genetic studies reported that some common variants located within BCL9 are associated with schizophrenia in the Chinese population, but not associated with bipolar disorder in the Caucasian population. Methods: Single nucleotide variant (SNP) prioritization sample was comprised of 575 patients with schizophrenia and 564 healthy controls with no personal or family history of psychiatric illness. For SNP association analysis, we used an independent Japanese sample set (replication sample) comprising 1464 cases and 1171 controls. For the analysis of cognitive performance, we investigated 115 cases and 87 controls using Continuous Performance Test (CPT-IP) and the Wisconsin Card Sorting Test Keio version (WCST). Meta-selectanalysis was performed using a combined Japanese total sample (N=3735) and a Chinese sample from a previous study. Results: In the replication sample set, we did not detect any association in 2 SNPs (rs672607 and rs10494252) and schizophrenia. Meta-analysis of rs672607 showed significant association (p-value 0.012, odds ratio 0.855). There was a significant (p<0.01) difference between the A/A and G carrier group of rs672607 in CPT mean d' (p=0.0092). Conclusions: We were able to detect evidence for an association between rs672607 in BCL9 and schizophrenia in the meta-analysis of Japanese and Chinese populations. Additionally, this common variant may affect cognitive performance, as measured by the CPT-IP in schizophrenia patients.