NKX3.1 is a prostate-specific transcription factor that is regulated by the androgen receptor in the presence of androgens. It functions as a tumor suppressor against the development of prostatic intraepithelial neoplasia and primary prostate tumors. Here, a recognized approach combining in silico analysis and chromatin immunoprecipitation (ChIP) was used to identify the genes directly regulated by NKX3.1 promoter binding in LNCaP cells. Quantitative PCR using ChIP-captured DNAs as templates verified a subset of NKX3.1 binding motifs. Thus, in the presence of androgens, significant NKX3.1 binding occurs to promoters of GPX2, QSCN6, SOD1, and SOD2 genes that contribute to oxidative stress regulation. Our data demonstrate that NKX3.1 is found in a DNA-bound state transiently at a basal level even in the absence of androgens; an increase in androgens promotes NKX3.1 binding, perhaps temporally rather than spatially, to the specific sites. The overall changes potentiate the transcriptional regulatory activity of NKX3.1, although they are dependent on the androgen receptor for the target promoters. The results suggest that NKX3.1 contributes to an antioxidant response by regulating the transcription of oxidative stress regulators by direct promoter binding.