We reported previously that bone morphogenetic protein 7 (BMP7) could induce epithelial-mesenchymal transition (EMT) in PC-3 prostate cancer cells grown in tissue culture plates. In this study, we examined BMP7-induced morphological and molecular expression changes that are characteristic of EMT using these cells under both two- (2D) and three-dimensional (3D) culture conditions. Filamentous outgrowths from spheroid structures that were formed from PC-3 cells in 3D cultures were strikingly evident when the spheroids were exposed to extracellular BMP7. This morphological change in 3D was accompanied by down-regulation of E-cadherin, which is an essential adhesion molecule for the integrity of epithelial phenotype. Invasiveness of the cancer cells was significantly enhanced with BMP7 treatment along with activation and up-regulation of proteases such as MMP1, MMP13, and urokinase plasminogen activator. Signal transduction of EMT conversion was examined by the use of certain pathway-specific inhibitors. Of the chemical inhibitors tested, inhibitors of PI3 kinase and Erk were found to suppress BMP-induced morphological changes both in 2D and 3D conditions. These results suggest that, besides the Smad signaling pathways, BMP-induced activation of PI3K and Erk contribute to EMT morphologic conversion of the PC-3 prostate cancer cells. Together, the results support the notion that the complexity of EMT may be better evaluated in terms of both spatial and temporal processes in 3D cell culture models that are physiologically more relevant than the cell growth in tissue culture plates.