The ISH and IHC assays for assessing HER2 are now recommended by the American Society of Clinical Oncologists and the College of American Pathologists, but there are an increasing number of published studies describing alternative diagnoses at the molecular level. Inspired by these studies, we established a laboratory-developed test (LDT) to analyze HER2 status not only at the gene expression level but also at the gene copy number level. The results were reported according to the concordant results of the DNA and RNA approaches. We also obtained fully agreeing results in ten blindly analyzed samples using the quantitative real-time PCR method and IHC. The topic of this short communication will hopefully contribute to allowing IVD-certified diagnostics based on HER2 gene expression profile or copy number to be tested in the Czech Republic as well.