Several genetic studies have shown an association between the 5-HT1A receptor gene (HTR1A) and major depressive disorder (MDD); however, results have been rather inconsistent. Moreover, to our knowledge, no association study on HTR1A and MDD in the Japanese population has been reported. Therefore, to evaluate the association between HTR1A and MDD, we conducted a case-control study of Japanese population samples with two single-nucleotide polymorphisms (SNPs), including rs6295 (C-1019G) in HTR1A. In addition, we conducted a meta-analysis of rs6295, which has been examined in other papers. Using one functional SNP (rs6295) and one tagging SNP (rs878567) selected with the HapMap database, we conducted a genetic association analysis of case-control samples (331 patients with MDD and 804 controls) in the Japanese population. Seven population-based association studies, including this study, met our criteria for the meta-analysis of rs6295. We found an association between rs878567 and Japanese MDD patients in the allele-wise analysis, but the significance of this association did not remain after Bonferroni's correction. We also did not detect any association between HTR1A and MDD in the allele/ genotype-wise or haplotype-wise analysis. On the other hand, we detected an association between rs6295 and MDD in the metaanalysis (P(Z)¼0.0327). In an explorative analysis, rs6295 was associated with Asian MDD patients after correction for multiple testing (P(Z)¼0.0176), but not with Caucasian MDD patients (P(Z)¼0.138). Our results suggest that HTR1A may not have a role in the pathophysiology of Japanese MDD patients. On the other hand, according to the meta-analysis, HTR1A was associated with MDD patients, especially in the Asian population. Keywords: case-control study; functional SNP; major depressive disorder (MDD); meta-analysis; serotonin 1A receptor gene (HTR1A); tagging SNP INTRODUCTION Altered serotonergic neural transmission is hypothesized to be a susceptibility factor for major depressive disorder (MDD). The evidence for such an association is discussed in more detail in reviews. 1,2 Several genetic studies have shown an association between the serotonin 1A (5-HT1A) receptor gene (HTR1A) and MDD; however, results have been rather inconsistent. A recent meta-analysis showed no association between HTR1A and MDD. 3 However, two very recent studies reported that rs6295 (C-1019G) in the promoter region of HTR1A, which regulates HTR1A transcription, 4,5 was associated with MDD in the Chinese population. 6,7 Moreover, to our knowledge, no association study of HTR1A and MDD in the Japanese population has been reported. Therefore, we examined the association between HTR1A and MDD in the Japanese, using the recently recommended strategy of 'genebased' association analysis. 8 Moreover, we conducted an updated