Recent studies have shown a unique chromosomal rearrangement that leads to the fusion of 5'-transmembrane protein serine proteinase-2 (TMPRSS2) with the EST-related gene (ERG) in prostate cancer. In this study, we used fluorescence in situ hybridization to evaluate TMPRSS2-ERG gene fusion in prostate cancer of different zonal origins. Radical prostatectomy specimens with multifocal prostate cancer were obtained from 30 patients who were treated at our institution. Two separate tumor foci in each specimen, one in the peripheral zone and the other in the transition zone, were selected for gene fusion analysis. The selected peripheral zone tumor foci had a mean Gleason score of 6.8 (range, 6-7) and a mean tumor volume of 1.2 cm(3) (range, 0.1-4.6 cm(3)). The selected transition zone tumor foci had a mean Gleason score of 6.7 (range, 5-8) and a mean tumor volume of 4.0 cm(3) (range, 0.5-9.0 cm(3)). ERG gene rearrangement was not observed in any transition zone tumors; however, it was found in the peripheral zone tumors in 13 cases (43%). In 10 cases, the rearrangement was associated with the deletion of the 5'-end of ERG. In conclusion, we found that TMPRSS2-ERG gene fusion is associated with the zonal origin of prostate cancer. This gene fusion is prevalent in prostate cancer arising from the peripheral zone, but is lacking in prostate cancer arising from the transition zone.