Invasive breast cancer is a heterogeneous disease sustained by intercorrelated and complex growth pathways. Classically, human breast carcinoma has been classified for therapeutic purposes in two distinct categories: one hormone-correlated, the other hormone-uncorrelated. However, the recent advancements of the technology applied to molecular biology by genomic and proteomic analyses have suggested that many more factors are involved in breast cancer growth and progression and that some clusters of these distinguish subgroups of patients at different prognosis. The knowledge of the diversities between tumor and normal tissue of origin is the key to identify novel targets for new selective therapeutic strategies. In fact, the principal goal of molecular-targeted therapy is the suppression of the transformed phenotype minimally affecting normal cells. This review focuses on the molecular targeting compounds directed against the known molecular pathways involved in breast cancer such as: type I growth factors (HER-2/neu; epidermal growth factor receptor [EGFR]), angiogenesis, cyclooxigenase-2 (COX-2) and farnesylation. Presently, trastuzumab is the first agent approved for therapy of HER-2/neu overexpressing tumors. Several other compounds directed against different targets have entered clinical evaluation and the preliminary results are here presented and commented. The major challenges on the clinical development of targeted therapy include the proper selection of patients, the identification of the optimal dosage and schedule of administration, the combinations with conventional treatments and the more appropriate therapeutic strategy.