In this paper, we describe the isolation and characterization of two PC3 subclones. One subclone, mr, showed an epithelial phenotype, the other, M1, showed a sarcomatous morphology. Transplanted into nude mice, mr developed tumors at a dramatically faster rate than M1. Comparing the two subclones, differentially expressed genes were identified, including E-cadherin, IL-8 and STAG1/PMEPA1. These genes were expressed at higher levels in mr than in M1.