Paclitaxel resistance remains a major challenge in the treatment of breast cancer. Six1 is a homeodomain-containing transcription factor invloved in the initiation, progression and metastasis of breast cancer. We herein investigate the relationship between Six1 and resistance of paclitaxel in this study. The results indicate that six1 is a mediator of the paclitaxel resistance in breast cancer. The expression level of Six1 in breast cancer cells correlates with their resistance to paclitaxel. On the one hand, forced overexpression of Six1 in Six1-low/paclitaxel-sensitive MCF-7 or HS578T breast cancer cells induce their resistance to paclitaxel treatment directly; On the other hand, knockdown of endogenous Six1 in Six1-high/drug-resistant BT-474 breast cancer cells sensitized these cells to paclitaxel treatment. Besides, Six1 overexpression confers resistance to paclitaxel-mediated apoptosis in breast cancer cells. Furthermore, clinical data and the publicly available breast cancer gene expression datasets display that the association of Six1 expression with paclitaxel sensitivity is clinically relevant. In conclusion, these data suggest that Six1 may function as an important modifier of the paclitaxel response in breast cancer cells, and serve as a potential target for overcoming paclitaxel resistance in breast cancer.