In the past 30 years, important advances have been made in the knowledge of breast cancer biology and in the treatment of the disease. However, the translation of these advances into clinical practice has been slow. With the advent of molecular-based medicine, it is hoped that the bridge between the bench and the bedside will continue to be shortened. Because breast cancer is a heterogeneous disease with wide-ranging subsets of patients who have different prognoses and who respond differently to treatments, the identification of patients who need treatment and the definition of the best therapy for an individual have become the priorities in breast cancer care. This article will review the crucial role of prognostic and predictive factors in achieving these goals. A critical review of classical and newer individual molecular markers, such as hormone receptors, HER2, urokinase-type plasminogen activator and plasminogen activator inhibitor 1, cyclin E, topoisomerase II, and p53, was performed, and the preliminary results obtained using the new gene expression profiling technology are described along with their potential clinical implications.