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Intratumoral heterogeneity of HER2 protein expression and HER2 gene amplification can negatively affect determination of HER2 status in a subset of invasive breast carcinomas. The frequency and clinical significance of HER2 genetic heterogeneity are unknown due to the lack of uniform criteria for diagnosis. Recent ASCO/CAP guidelines (2009) define HER2 genetic heterogeneity as the presence of between 5% and 50% of tumor cells with a HER2/CEP17 ratio >2.2. We describe a tool (a customized Excel spreadsheet) for easy and reproducible diagnosis of HER2 genetic heterogeneity according to ASCO/CAP criteria. Our tool may be useful for routine HER2 diagnostics and for studies to analyse the hitherto unknown predictive significance of HER2 genetic heterogeneity.