To evaluate the controversial, putative associations between the three common polymorphisms (promoter uVNTR，T941G，(CA) repeat) of MAOA and mood disorders (major depressive or bipolar disorders) by systematically meta-analyzing published case-control association studies. We queried PubMed using the key words “MAOA”, “Monoamine oxidase A”, “association” and “depression” or “bipolar”. Nine studies on uVNTR, seven studies on T941G, and eight studies on CA met the inclusion criteria. The meta-analysis was performed by gender and ethnicity. Our meta-analysis showed a significant association between uVNTR and MDD for the Asian group (OR=1.23 (1.02-1.47), p=0.03) and male Asian group ( OR=1.47(1.06-2.05), p=0.02). For the T941G polymorphism, we found a significant association with BPD in the Caucasian group (OR=1.28(1.01-1.62), p=0.04) and female Caucasian group (OR=1.36(1.031-1.81), p=0.03). For the CA polymorphism, we identified significant associations with BPD in all Caucasians for the overall alleles and for the specific alleles in a6 (OR=1.35(1.11-1.64), p=0.002) and in female Caucasians for the overall alleles and for the specific alleles in a2 (OR=0.65(0.48-0.90), p=0.009), a5 (OR=1.44(1.04-1.99), p=0.03), and a6 (OR=1.41(1.12-1.78), p=0.004). Our meta-analysis suggests a significant association of the MAOA gene with major depressive disorder and bipolar disorder within specific groups, indicating that these three polymorphisms of the MAOA gene may be associated with mood disorders by gender and ethnicity. Moreover, our systematic meta-analysis has revealed that although MAOA may be a common candidate gene for mood disorders, different polymorphisms and alleles appear to play different roles in major depressive disorder and bipolar disorder.