Alterations in brain-derived neurotrophic factor (BDNF)-signaling pathways may play an important role in the pathophysiology of major depressive disorder (MDD). Several lines of evidence have suggested that gene-gene interactions may confer susceptibility to MDD. The aim of this study was to analyze the single and combined effects of genes in the BDNF signal-transduction pathway on MDD in a Chinese population. We recruited 447 patients with MDD and 432 age- and gender-matched control subjects. Five SNPs in three BDNF signal-transduction pathway genes (BDNF, GSK3B and AKT1) were used in association analyses. An allelic association between the GSK3B SNP rs6782799 and MDD was found in our sample (allelic: chi(2) = 5.24, P = 0.022, corrected P = 0.107; genotypic: chi(2) = 5.55, P = 0.062) with an odds ratio (OR) of 1.25 (95% confidence interval (CI) 1.03-1.52). Further gene-gene interaction analyses showed a significant effect of a two-locus BDNF/GSK3B interaction with MDD (GSK3B rs6782799 and BDNF rs7124442) (corrected P = 0.011), and also for a three-locus interaction (GSK3B rs6782799, BDNF rs6265 and BDNF rs7124442) (corrected P = 0.019). Individuals carrying the combination of two risk alleles showed an OR value of 4.00 (95% CI 2.05-7.79), while those with the combination of three risk alleles gave the largest OR value of 4.46 (95% CI 2.15-9.24). Taken together, these findings support the assertion that the GSK3B gene is an important susceptibility factor for MDD in a Han Chinese population.