Cancer treatment has revolutionized from a "one size fits all" approach to a more individualized approach with the advancement of medicine and molecular biology. Several predictive and prognostic factors have been studied and applied to clinical practice to assist clinicians in cancer management. In breast cancer therapeutics, the appearance of biomarkers such as expressions of hormone receptor and human epidermal growth factor (HER) receptors has modified treatment strategies from chemotherapy to molecular-targeted therapy including endocrine therapy and anti-HER therapy. With better understanding of the molecular level of tumorigenesis, cancer pathogenesis and metastases, several novel biomarkers such as cyclo-oxygennase-2 enzyme and tyrosine kinases have been discovered and new anti-cancer agents have been introduced into the currently available treatments. The change has also modified pre-operative treatment for locally advanced and early breast cancers. The neo-adjuvant treatment indeed provides an excellent platform for translational research which is a widely used research method in clinical research. The study of gene and protein expressions from tissue and blood samples collected before, during and after neo-adjuvant treatment provides a lot of keys to decipher the signaling pathways and discover novel biomarkers which are essential for development of new drugs and prediction of the clinical outcome of therapy. The addition of gene expression profiling to conventional predictive factors will give more prognostic information to clinicians for better management of the disease.