One of the prognostic and predictive factors in invasive breast carcinomas is determination of the HER2/neu proto-oncogene amplification or HER2 protein overexpression. HER2 amplification/overexpression is associated with a more aggressive disease course, greater likelihood of recurrence and generally poor prognosis. The authors compared the specificity, simplicity of a given procedure and method standardization, the simplicity of evaluation the results of each in situ hybridization method and time needed for performing the test. Sixty-three cases of infiltrating breast carcinoma from surgically excised tumors and core needle biopsies were included in the study. The first step was the determination of HER2 status by immunohistochemistry. The patients with moderate (2+) and strong (3+) overexpression of HER2 protein were chosen for determining HER2 amplification by three methods of in situ hybridization: FISH, CISH and in situ hybridization with silver autometallography. The statistical analysis revealed a good agreement between IHC and ISH methods and among ISH methods. The results indicate that all in situ hybridization methods are equivalent tools for evaluating HER2 gene amplification in archival material. There is no clear answer which method is the best assay to determine HER2 marker status, although the authors present some advantages and disadvantages of all the described techniques and a proposed algorithm for choosing a method for a given laboratory.