Background: Stemness in sarcomas is coordinated by the expression of pluripotency factors, like SOX2, in cancer stem cell (CSC) subpopulations. The role of SOX2 in tumor initiation and progression has been well characterized in osteosarcoma. However, the pro-tumorigenic features of SOX2 have been scarcely investigated in other sarcoma subtypes. Methods: shRNA and cDNA lentiviral constructions were used to deplete and overexpress SOX2 in a model of undifferentiated pleomorphic sarcoma (UPS). In addition, we introduced a reporter system (SORE6) which allows to detect and isolate viable cells expressing SOX2 and/or OCT4 in the UPS model and patient-derived chondrosarcoma lines. Functional CSC characterization included tumorsphere formation, in vivo xenograft growth assays, and pharmacologic testing of the effects of doxorubicin, placlitaxel, trabectedin or the mithramycin analogue EC8042. Immunohistochemical analysis of a cohort of 88 formalin-fixed and paraffin-embedded sarcoma samples was performed to correlate SOX2 expression with clinical parameters. Findings: SOX2 depletion dramatically reduced the ability of sarcoma cells to form tumorspheres and to initiate tumor growth in vivo. Conversely, SOX2 overexpression resulted in increased in vivo tumorigenicity. In sarcoma patients, SOX2 expression was associated to advanced disease stages, aggressive phenotypes and lower survival. Finally, SORE6+ cells were significantly more tumorigenic than the SORE6- population and EC-8042 effectively targeted SORE6+ cells in vitro and in vivo. Interpretation: SOX2 is a pro-tumorigenic factor with prognostic potential in sarcoma. Moreover, SORE6 transcriptional activity is a bona fide CSC marker in sarcoma and constitutes an excellent biomarker for evaluating the efficacy of anti-tumor treatments on CSC subpopulations. Funding Statement: This work was supported by the Agencia Estatal de Investigacion (AEI) [MINECO/Fondo Europeo de Desarrollo Regional (FEDER) (SAF-2016-75286-R to R.R.), ISC III/FEDER (Miguel Servet Program CPII16/00049 to R.R., Sara Borrell Program CD16/00103 to S.T.M. and PI16/00280 and PI19/00560 to J.M.G-P) and Consorcio CIBERONC CB16/12/00390)] and the Plan de Ciencia Tecnologia e Innovacion del Principado de Asturias/FEDER (IDI/2018/155) to J.P.R. PharmaMar and EntreChem also provided support. Finally, the authors acknowledge the Principado de Asturias BioBank (PT17/0015/0023), financed jointly by Servicio de Salud del Principado de Asturias, Instituto de Salud Carlos III and Fundacion Bancaria Cajastur and integrated in the Spanish National Biobanks Network, for its collaboration. Declaration of Interests: The authors declare they have no competing interests. Ethics Approval Statement: All experimental protocols have been performed in accordance with institutional review board guidelines and were approved by the Institutional Ethics Committee of the Principado de Asturias. All samples from human origin were obtained upon signed informed consent. All experimental protocols were carried out in accordance with the institutional guidelines of the University of Oviedo and were approved by the Animal Research Ethical Committee of the University of Oviedo prior to the study.