Gender differences in various clinical features of schizophrenia have been noted and estrogen has been regarded to play important roles. A few previous studies on the association between estrogen receptor (ER) genotypes and schizophrenia focused mainly on ER α gene but failed to report consistent results. The present study was designed to analyze the differences in the frequencies of both ERα and ERβ gene polymorphisms in subjects with schizophrenia compared to healthy controls among Korean population. Moreover, we investigate the association between different genotypes of ER genes and various clinical variables of schizophrenia. We observed that PvuII and XbaI polymorphisms of ERα gene showed significant differences between patients with schizophrenia and control groups (p=0.006). Among clinical variables, only the age of onset was related to RsaI genotype of ERβ gene (p=0.039). In conclusion, the present study suggests that ERα gene polymorphisms may be associated with the pathogenesis of schizophrenia and RsaI AA genotype of ERβ might have protective effect on age at onset of schizophrenia in Korean patients with schizophrenia.