Abstract This study aimed to compare two methods of quantitative polymerase chain reaction (qPCR) using the intercalating SYBR Green dye and TaqMan hybridization probes to determine the amount of the HER2 gene (human epidermal receptor) in breast tumours. Methods--- The experiments were carried out with 32 validated samples of breast cancer and two gastric cancer cell lines. An immunohistochemical (IHC) assay was used to evaluate the accuracy of the RT-PCR methods. Results--- The obtained results show that real-time PCR with the TaqMan probes allows the use of a small amount of DNA (≥0.4 ng/µl) to determine the overexpression of the HER2 gene. Real-time PCR with SYBR Green allowed us to determine the minimum number of false negatives resulting from the absence of marker expression in tumour tissue. Conclusions--- The full correspondence of the results of the RTPCR and immunohistochemistry methods obtained for the cell line samples makes it possible to introduce the qPCR method into clinical practice for use in detecting the HER2/neu gene content.