This study examined the relationship between a MnSOD gene (MnSOD) polymorphism (Ala-9Val) and mood disorders such as major depressive disorder (MDD) and bipolar I disorder (BD). Eighty patients with BD, 61 patients with MDD and 106 healthy controls were enrolled in this study and genotyped using a polymerase chain reaction-based method. The patients with MDD and BD, and the controls had a similar distribution of the genotypes and alleles in the Ala-9Val MnSOD polymorphism. The combined analysis (MDD plus BD) also failed to find any association between the Ala-9Val MnSOD polymorphism and mood disorders. Subgroup analyses according to the clinical variables such as the family history, age at onset, psychotic features and suicide history failed to identify any association with the Ala-9Val MnSOD polymorphism. This preliminary data suggests that at least in the Korean population, the Ala-9Val MnSOD polymorphism is not associated with the development of mood disorders or their clinical parameters. However, more study with a larger population sample will be needed.