We aimed to document the pathological characteristics of breast cancer (BC) cases with different scores of HER2 by immunohistochemistry (IHC), as well as to establish a relationship between HER2 expression and HER2 amplification by in situ hybridization (ISH). A cohort of 258 primary BC cases was evaluated for HER2 gene amplification with bright-field ISH. All HER2-negative and HER2-positive cases by IHC were concordant with the ISH classification. BC cases with score of 0 had lower average of HER2 copy number compared to cases with score of 1 + . HER2-equivocal cases by IHC had intermediate pathological characteristics between HER2-negative and HER2-positive cases. About 12% of HER2-equivocal cases were classified as ISH-positive. HER2-equivocal cases with HER2 gene amplification had proliferation index, HER2/CEP17 ratio, and average of HER2 copy number between HER2-equivocal cases without HER2 gene amplification and HER2-positive cases by IHC. Additionally, HER2-equivocal cases with HER2 amplification had score of 2 + in at least 50% of the total tumor area, with a proportion of ISH-positive cases increasing with the amount of score of 2 + present in the tumor. The quantification of score of 2 + in the tumor predicted the ISH classification with an AUC of 0.902. A logistic regression model using the same HER2 quantification and the nuclear score was able to increase the abovementioned prediction to an AUC of 0.929. As such, we were able to link HER2 quantification by IHC and morphological analysis with HER2 amplification by ISH. © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.