Over-expression of the human epidermal growth factor receptor-2 (HER2/neu) has been observed in many cancers, and is associated with a poor prognosis. Recent adjuvant treatment with anti-HER2 monoclonal antibodies in breast cancer has increased the demand for an evaluation of the HER2/neu status in breast cancer. The aim of this study was to investigate the HER2/neu status in breast cancer by a real-time quantitative polymerase chain reaction (PCR) method using LightCycler (Roche Diagnostics, Mannheim, Germany). DNA samples from the fresh tumor tissues of 27 patients with breast cancer were analyzed in parallel using immunohistochemistry (IHC) and the other prognostic parameters including estrogen receptor, progesterone receptor, cytokeratin, and DNA ploidy. Ten (37%) out of 27 cases tested were positive for HER2/neu, while 16 (73%) out of 22 tested positive through an IHC study. The correlation between the DNA aneuploidy and the positive results for HER2/neu were only observed using the real-time PCR method (p < 0.05). There was no significant correlation between the HER2/neu status and the S-phase fractions of the DNA ploidy or other parameters. This study demonstrated that there is marked discordance in the results for the HER2/neu status according to the various methods used. Real-time quantitative PCR for HER2/neu appears to be clinically useful due to its simplicity and ability to produce rapid results.