NKX3.1, a prostate-specific gene, plays an important role in prostate development and carcinogenesis. However, its precise function has not been established. In present study, we transfected the NKX3.1 eukaryotic expression plasmid (pcDNA3.1-NKX3.1) into human prostate cancer cells PC-3, which lack of NKX3.1 expression, and established stable transfectants. Then, we investigated the influence of NKX3.1 on the cell growth, cell migration and colony formation efficiency. The results showed that restoration of NKX3.1 expression inhibited proliferation and invasion activities of PC-3 cells. Further, a cDNA microarray containing 22,000 human genes was used to identify the gene expression differences. The results showed that there were 1,953 genes showing more than a two-fold difference in expression. Subsequent ontological analysis revealed that a large proportion of the classified genes were related to cell growth, cell signal and cell invasion. Finally, the expression of Caspase-3, Bcl-2, P27, Cdk6 and AMACR, randomly selected genes from microarray data, was validated by RT-PCR and western blot. Collectively, our results first analyzed the gene expression profile in PC-3 cells induced by NKX3.1 and indicated that NKX3.1 might exert its function by regulating the expression of relative genes.