The purpose of this study was to assess the usefulness of HER2 levels in ultrasonographically guided fine-needle aspiration biopsy (US-FNA) aspirates of axillary lymph nodes (ALNs) in the determination of lymph node metastasis or the characterization of primary breast cancer, and to correlate the HER2 levels in US-FNA aspirates (FNA-HER2s) of metastatic ALNs with the HER2 statuses of corresponding primary breast cancers. An institutional review board approved the study. Between January and October 2010, 164 patients with 167 ALNs examined by US-FNA were included. FNA-HER2s of ALNs were measured by chemiluminescence immunoassay, and they were correlated with cytologic/final diagnoses. Receiver operating characteristics (ROC) curve analysis was performed to evaluate the diagnostic ability to differentiate benign and metastatic ALNs. Additionally, FNA-HER2s of metastatic ALNs were correlated with HER2 status and other clinicopathologic variables of the primary breast cancers. Among the 167 ALNs, 138 were metastatic and 29 were benign. The mean FNA-HER2 (6.3 ng/ml) of metastatic ALNs was higher than that of benign ALNs. All 29 benign ALNs showed no measurable value of FNA-HER2 (0.0 ng/ml). The area under the ROC curves of FNA-HER2 of ALNs was 0.679 for the diagnosis of ALN metastasis. The FNA-HER2 statuses of 108 metastatic ALNs (79.4%) were concordant with the HER2 statuses of the corresponding primary breast cancers. In a subgroup analysis of HER2-positive cancers with ALN metastasis, distant metastasis was significantly associated with FNA-HER2-negativity of metastatic ALNs (P = 0.04). Although FNA-HER2 of ALNs did not improve the diagnostic performance of FNA cytology in preoperative diagnosis of ALN metastasis of overall patients, FNA-HER2-positive metastatic ALNs were significantly associated with HER2-positivity of primary breast cancers. Additionally, FNA-HER2 analysis of ALN may help to develop more personalized treatment protocol for breast cancer patients by determining the concordance or discordance of HER2 status between primary cancers and metastatic ALNs.