The genetic pathogenesis of major depressive disorder (MDD) has not been elucidated. It has been proposed that brain-derived neurotrophic factor (BDNF), as a member of the neurotrophin family, may be involved in the etiology and antidepressant response of MDD. The present study investigated the possible presence of an association between the BDNF gene and MDD. Single-marker transmission disequilibrium test (TDT), pairwise-SNP linkage disequilibrium (LD) and haplotype-based TDT analyses were performed on single nucleotide polymorphisms (SNPs) rs6265, rs10835210 and rs2030324 in 105 Chinese trios. No significant associations with MDD were demonstrated for three SNPs. Pairwise LD analysis revealed substantial LD among three SNPs. Multiple-marker TDT analysis indicated that there was no association between the haplotypes from rs6265-rs10835210-rs2030324 and MDD. The statistical power of the present study was calculated so we had an idea what kind of effects could be identified. We conclude that SNPs rs6265, rs10835210 and rs2030324 of the BDNF gene are unlikely to play a critical role in the pathogenesis of MDD.