Purpose: We investigated the significance of CD24 and CD44 expression for predicting responses to chemotherapy and prognosis in primary breast cancer patients.Patients and Methods: Diagnosis of breast cancer was confirmed by core needle biopsy, and immunohistochemical studies were performed.Preoperatively, patients received anthracyclinecontaining chemotherapy.Expression of CD44 and CD24 was assessed immunohistochemically and the relationship with chemotherapy response and with prognosis was analyzed.Results: Between 2001 and 2004, 139 women were enrolled in this study.In the correlation analysis, CD24 expression was negatively associated with pathological response to chemotherapy (p=0.0003).A machine learning technique with an alternating decision tree (ADTree) showed that four logical rules are involved in predicting the response depending on the combination of CD24, HER2, tumor stage,CD44, progesterone receptor, and patient age.In the survival analysis, patients having CD44 (++) showed a significantly favorable prognosis as compared with others (p=0.0002).A multivariate analysis showed that CD44 expression had an independent prognostic value (p<0.001).Conclusion: We found a significant correlation between CD44 expression and prognosis and between CD24 expression and response to chemotherapy.CD24 and CD44 expressions would be useful predictive markers, although further studies are needed.