Brain-derived neurotrophic factor (BDNF) is a nerve growth factor that has antidepressant-like effects in animal models and may be implicated in the etiology of mood-related phenotypes. A functional polymorphism (Val66Met) in the BDNF gene was demonstrated to influence BDNF's secretion and function, as well as mood and cognitive related phenotypes. However, previous genetic association studies of Val66Met polymorphism in the clinical risk of mood disorders have been complicated, possibly due to phenotypic diversity, underpowered statistical association or ancestry-specific effects. Here, we collected mood phenotypic and genetic data in over 90,000 individuals from diverse ethnic groups and conducted a systematic meta-analysis. The results showed that the Val66Met polymorphism was significantly associated with BPD in Europeans (Pmeta = 0.0029, OR = 1.136), but not in Asians (Pmeta = 0.443). Also, it appears that the risk for MDD conferred by BDNF is waning, as the Val66Met variant was not associated with MDD in either European or Asian samples (Pmeta > 0.5).