The aim of this study was to evaluate the role of several biological and histological markers (topoisomerase IIalpha, MIB-1, E2F, apoptotic index, APE/ref-1, p53, Her-2/neu, estrogen and porgesterone receptors, and histological grading) as predictors of pathologic response after anthracycline-based chemotherapy for breast cancer. A series of 50 consecutive breast cancer patients receiving anthracycline-based primary chemotherapy were retrospectively studied. Biological markers were assessed by immunohistochemistry (and by TUNEL assay for apoptotic index) in pre-treatment core biopsies and post-treatment surgical samples. The expression of topoisomerase IIalpha, E2F, MIB-1, estrogen and progesterone receptors decreased, while APE/ref-1 staining increased after treatment. Higher topoisomerase IIalpha (P=0.007) and lower APE/ref-1 (P=0.04) expression were associated with better pathologic response.