Neoadjuvant (preoperative) chemotherapy is an interesting research tool which allows investigators to test new drugs and/or new schedules with a validated surrogate endpoint, pCR. It also represents an ideal model to evaluate the relationships between treatments and tumor biomarkers. Recent publications have shown that new molecular classifications of breast cancer (intrinsic subtypes) have an important prognostic and predictive value. Using microarrays for gene expression profiling seems to be the best way to perform this classification; nevertheless such assays are not optimally available for common clinical practice. The IHC-based classification systems are still useful, as fresh tissue is not normally available in clinical practice, and has been shown to correlate well with intrinsic classification using gene expression microarrays. Recently the PAM50 gene set provided a risk of relapse score not only in ER-positive, node negative patients (similarly to the Oncotype Dx Recurrence Score) but also in the ER negative disease. Additionally, the PAM 50 assay was highly predictive of neoadjuvant response when considering all patients. This assay added significant prognostic and predictive value to pathologic staging, histologic grade, and standard clinical molecular markers while using an easy technique that can be performed in clinical practice because the qRT-PCR assay can be performed using FFEP tissue.