We compared the breast core needle biopsy and the resection specimen with respect to estrogen (ER), progesterone (PR) and human epidermal growth factor receptor 2 (HER2) status to identify predictors for discordant findings. We retrospectively collected data from 526 newly diagnosed breast cancer patients. ER, PR and HER2 status had been assessed in both the core needle biopsy and resection specimen. The assessment of ER by immunohistochemistry (IHC) in core needle biopsy was false negative in 26.5% and false positive in 6.8% of patients. For the PR status the false negative and false positive results of core needle biopsy were 29.6% and 10.3%, respectively. The results of the HER2 status, as determined by IHC and silver in situ hybridization (SISH), were false negative in 5.4% and false positive in 50.0%. We need to be aware of the problem of false negative and false positive test results in ER, PR and HER2 assessment in core needle biopsy and the potential impact on adjuvant systemic treatment. With current techniques, we recommend using the resection specimen to measure these receptors in patients without neoadjuvant treatment. A better alternative might be the use of tissue microarray, combining both core needle biopsy and resection specimen.