Sentinel lymph node (SLN) status is highly predictive of overall axillary lymph node involvement in breast cancer. Historically, SLN-positive patients have undergone axillary lymph node dissection in a second surgery. Intraoperative SLN analysis could reduce the cost and complications of a second surgery; however, existing histopathological methods lack standardization and exhibit poor sensitivity. Rapid molecular methods may lead to improved intraoperative diagnosis of SLN metastasis. In this study, we used a genome-wide gene expression analysis of breast and other tissues to identify seven putative markers for detecting breast cancer metastasis. We assessed the utility of these markers for identifying clinically actionable metastases in lymph nodes through reverse transcriptase-polymerase chain reaction analysis of SLNs from 254 breast cancer patients. Polymerase chain reaction signals were compared to pathology on a per-patient basis. The optimal two-gene combination, mammaglobin and cytokeratin 19, detected clinically actionable metastasis in breast SLNs with 90% sensitivity and 94% specificity. Application of stringent criteria for identifying presumptive hematoxylin-and eosin-positive samples increased sensitivity and specificity to 91 and 97%, respectively. This study represents the first comprehensive demonstration of the utility of gene expression markers for detecting clinically actionable breast metastases. An intraoperative molecular assay using these markers has the potential to significantly reduce second surgeries for patients undergoing SLN dissection. Breast cancer is second only to lung cancer in mortality among women worldwide.1 In the care of this significant disease, the evaluation of blood, bone marrow, and lymph nodes for the presence of metastatic cells is an important component of disease characterization and management.2-6 The method for assessment of these peripheral tissues is largely dependent on histological and cytological methods. Detection of metastasis in lymph nodes is typically accomplished by hematoxylin and eosin (H&E) and antibody staining of lymph node sections.7,8 Analysis of bone marrow samples, although still in development, currently involves antibody staining of cytological smears. For some time, there has been discussion about the potential for the use of molecular biological tools to supplement or to improve existing methods.9 Molecular methods such as reverse transcriptase-polymerase chain reaction (RT-PCR) offer increased analytical sensitivity compared with standard histological methods. 10 -12 In addition, nucleic acid-based detection methods such as real-time PCR offer the potential of rapid and sensitive point-of-care testing and the application of objective quantitative assay cut-offs.A clear intersection between these features is the intraoperative assessment of sentinel lymph nodes (SLNs) for the presence of clinically actionable metastasis, a level of metastasis that would be expected to consistently lead to a subsequent axillary lymph node (ALN) dissecti...