Background We explored whether cell signaling pathways related to drug resistance were activated in the stem-like cells ALDHhiCD44+ or not, and analysed the relationship between ALDHhiCD44+ cells and pathological features. Methods ALDHhiCD44+ cells and non-stem like cells ALDHlowCD44+ were separated by fluorescence-activated cell sorting from MDA-MB-231 cells. mRNA expression for Notch1 and β-catenin were estimated with Q-PCR. An immunohistochemical panel was used in patients with invasive breast carcinoma to evaluate the correlation with ALDHhiCD44+ cells with line correlation analysis. Findings The mRNA levels of Notch1 and β-catenin were higher in ALDHhiCD44+ cells than in ALDHlowCD44+ cells (p Interpretation The Notch and Wnt/β-catenin signaling pathways were abnormally activated in breast cancer stem like cells and were highly correlated with Ki67.