Core biopsies are commonly used in the diagnosis of breast cancer and often are the only sample for providing prognostic and predictive markers prior to neoadjuvant chemotherapy. We retrospectively studied 87 patients with breast cancer to compare the concordance rates for tumor type, grade, estrogen receptor/progesterone receptor (ER/PR), p53 status and Her2/neu by immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) between core and excisional biopsy specimens. The histologic type of cancer had a 100% concordance rate between core and excisional biopsy specimens. The concordance rate of modified Bloom-Richardson score between core and excisional biopsy specimens was 77%, ER was 95%, PR was 89%, and p53 was 86%. The concordance rate for Her2/neu by IHC was 96% and that for FISH was 100% between the core and excisional biopsy specimens. Although breast cancer may have heterogeneous histological and immunohistochemical findings, our study shows that relatively high concordance rates can be obtained when comparing core and excisional biopsy specimens.