Breast cancer stem cells (CSCs) are important element in the tumorigenesis and relapse. Long non-coding RNAs (lncRNAs) had been proved to regulate the breast cancer carcinogenesis. In present study, our research team aims to investigate the deepgoing role of SOX21-AS1 on breast CSCs properties and carcinogenesis. Human lncRNA microarray analysis and RT-PCR showed that SOX21-AS1 was up-regulated in breast cancer tissue. Moreover, the overexpression of SOX21-AS1 indicated the poor prognosis of breast cancer patients. Loss-of-function experiments revealed that SOX21-AS1 knockdown reduced the stem factors (Nanog, LIN28, Oct4 and SOX2) and CD44+/CD24â rate, suggesting the inhibitory role on breast CSC properties and selfrenewal ability. Besides, SOX21-AS1 knockdown inhibited the proliferation, invasion and tumor growth of breast cancer CSCs in vitro and in vivo. Bioinformatics online tools and luciferase reporter assay validated that miR-429 targeted SOX21-AS1 and SOX2 mRNA 3âČ-UTR, indicating the modulation of SOX21-AS1 and miR-429 on SOX2 protein expression. In summary, results conclude that lncRNA SOX21-AS1 modulates breast CSCs properties and carcinogenesis via targeting SOX2, providing a novel insight and therapeutic target for breast cancer.www.impactjournals.com/oncotarget/