To sort and identify side population (SP) cancer stem cells (CSC) in human prostate cancer (PCa) cell lines. Stem-like cells were isolated from five PCa cell lines Du145, IA8, LNCaP, TSU-Pr and PC-3 using FACS based on CD133+ CD44+ immunophenotype and SP in Hoechst staining. The in vitro growth pattern and tumorigenicity of SP stem cells were verified by soft agar colony-formation trial. LNCaP/SP cells were selected for further identification of stem cell properties using immunostaining, proliferation and invasion assay. Eventually, tumorigenicity and metastasis ability of LNCaP/SP were confirmed by xenograft experiments. The percentages of CSCs of the CD133 CD44 + immunophenotype were extremely low in the five PCa cell lines. On the contrary, the percentages of the isolated SP cells were significantly higher in Du145 ([0.15 +/- 0.02]%), IA8 ([0.60 +/- 0.07 ]%), LNCaP ([0.8 +/- 0.1]%) and TSU-PrL ([2.0 +/- 0.4]%), but none was detected in PC-3. Besides, IA8/SP, LNCaP/SP and TSU-PrL/SP cells showed a significantly greater colony-forming efficiency than non-side population (NSP) cells (P < 0.05). Compared with LNCaP/NSP cells, LNCaP/SP cells exhibited high expressions of integrin alpha2, Nanog, CD44, OCT4 and ABCG2, remarkably enhanced invasive and proliferative potentials in vitro, and markedly increased tumorigenicity and metastasis (P < 0.01). SP sorting is more suitable than CD133+ CD44+ selection for enriching CSCs from PCa cell lines, and LNCaP/ SP represents a typical CSC population.