The presence of arachidonate 12-lipoxygenase (12-LOX) potentiates prostate cancer (PCa) progression and therefore may be a good therapeutic target and/or a potential diagnostic predictor for PCa. In this study, we examined the expression of 12-LOX in PCa stem cells (PCa SCs) to test if it can serve as a unique marker and therapeutic target for PCa SCs. To this end, we isolated the cancer stem cell-like side population (SP) cells from the human PCa cell line DU-145 by a flow cytometry-based SP technique. The isolated DU-145 SP cells comprised a small population of the DU-145 cells. The SP cells had an up-regulation of ATP-binding cassette sub-family G member 2 (ABCG2) which enables these cells to efflux vital dyes and chemotherapeutic drugs. Furthermore, we detected a strong up-regulation of 12-LOX in these DU-145 SP cells compared to the parental DU-145 cells by RT-PCR and Western blot approaches. We also detected 12-LOX overexpression in PCa SCs in human PCa tissue samples by paraffin-section based immunofluorescent 4-channel confocal microscopy. However, no 12-LOX was detected in normal prostate epithelial SCs in normal prostate tissue samples. These multiple lines of evidence support the possibility that 12-LOX may serve as a unique marker and therapeutic target for PCa SCs.