Sentinel lymph node (SN) biopsy is part of the staging procedure in breast cancer patients. In this study, we compared an intraoperative tool named one-step nucleic acid amplification (OSNA) to our routine histological investigation. OSNA consists of a short homogenization step followed by amplification of cytokeratin (CK) 19 mRNA directly from the lysate. To evaluate the performance of OSNA in comparison to histology, analysis of 343 axillary lymph nodes (ALN) from 93 breast cancer patients was performed with both methods. Discordant samples were subjected to other methods. If these tests supported the OSNA results, these samples were excluded from the study. The concordance rate was 91.8%, sensitivity 98.1%, and specificity 90.8% before and 95.5%, 100%, and 95.6%, respectively, after discordant case investigation. Our results show that OSNA is an excellent method for the detection of metastases in lymph nodes and can be applied as an intraoperative diagnostic approach.