Abstract BACKGROUND HER2 overexpression drives tumor aggressiveness and poor prognosis, serving as a crucial therapeutic target in various malignancies. While HER2’s role in breast cancer metastasis and prognosis is well-documented, its heterogeneity in brain metastases (BM) across different primary tumors remains understudied. This investigation examined HER2 status in matched primary cancers and BM across multiple cancer types to evaluate HER2 alterations during metastases. MATERIAL AND METHODS We conducted a retrospective analysis of 185 matched primary tumor-BM pairs. HER2 expression was assessed using immunohistochemistry (IHC), with equivocal cases (IHC 2+) further evaluated by silver-enhanced in situ hybridization (SISH). We analyzed associations between HER2 positivity, clinicopathological factors, and survival outcomes. RESULTS Of the 185 matched cases, lung, breast, and colorectal cancers were predominant, with breast cancer showing the highest HER2 positivity rate (61.5%, P < 0.001). HER2 positivity was detected in 14.1% (26/185) of primary tumors and 15.1% (28/185) of BM with a 7.6% (14/185) discordance rate between primary and metastatic sites. HER2 positivity in BM significantly correlated with age, primary cancer type, and BM location (P = 0.040, P < 0.001, P = 0.045, respectively). Age, BM location, BM size, BM multiplicity, and presence of other organ metastases were identified as independent prognostic factors. CONCLUSION Our findings reveal significant HER2 heterogeneity between primary tumors and matched BM across cancer types. The observed discordance in HER2 status, particularly notable in breast cancer, underscores the necessity of HER2 status reassessment in BM for optimal targeted treatment strategies.