It has been proposed that an MAOA abnormality may be an important factor in the development of major depressive disorder (MDD). Various polymorphisms of the MAOA gene have been investigated for possible associations with mood disorders, but results have been inconsistent. The goal of the present study was to investigate whether polymorphisms of the MAOA gene are associated with MDD or alternatively with different clinical subgroups of MDD. A total of 590 Han Chinese subjects in Taiwan (312 controls and 278 MDD patients) were recruited. Among the males, there were no associations with MAOA polymorphisms. Among the females, an association was found between MAOA polymorphisms and severe MDD (P=0.041 for uVNTR and 0.017 for EcoRV (rs1137070), respectively). However, in analyses of haplotype frequencies and multiple logistic regression, MAOA polymorphisms were not associated with either MDD or its subgroups. The results suggest that MAOA polymorphisms do not play a major role in the pathogenesis of MDD or its subgroups. However, a potential role for a minor association with some specific subgroups and with different ethnic samples needs to be explored further.