In this study, we performed a systematic comparison of six breast cancer cell lines representing different molecular subtypes, including luminal A (T47D and MCF-7), luminal B (BT-474), HER2-OE (AU-565) and triple-negative/basal-like subtype (MDA-MB-231 and Hs578T) for CD44, CD24 expression and ALDH activity. The gene discussed is CD44; the disease is breast cancer.