In this study, we try to detect and isolate the cancer stem cell-like side population cells (SP) from the laryngeal carcinoma cell line and primary laryngeal carcinoma and explore the clinical implications of SP cells in laryngeal carcinoma. The SP cells and non-side population cells (NSP) cells were sorted by Hoechst 33342 through FACS. The proliferation capacity, invasion ability, migration ability, and tumorigenic activity of the SP cells were evaluated. In addition, the association between the SP cells ratio and the prognostic factors of laryngeal cancer was analyzed. As a result, the percentage of the SP cells in Hep-2 cells was 5.1%. The SP cells depicted float colonies, but the NSP cells failed to generate the typical cell spheres. The clone formation ratios were 47.47 ± 10.20% vs. 4.98 ± 1.41% in the flat plates and 46.82 ± 5.67% vs. 12.53 ± 3.51% in the soft agar for SP and NSP cells (P = 0.01 and 0.01). The SP cells depicted a higher migrating potency than the NSP cells in both the transwell assay and scarification test (all P < 0.05). The matrigel invasion assay showed that the artificial basement membrane penetration rate of SP cells was 39.04 ± 4.78%, which was higher than 25.16 ± 4.63% of the NSP cells (P < 0.05). Only 10(3) SP cells were able to form tumors in mice, whereas 10(4) NSP cells failed to form tumors. The SP cells were correlated with the differentiation, lymph node metastasis, and clinical stage of the laryngeal cancers. In conclusion, SP cells may be a potential prognostic factor of laryngeal cancer.