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BACKGROUND/AIM To evaluate whether core needle biopsy specimens (CNBS) would be better than surgical specimens (SS) for evaluating phosphoproteins as biological markers in breast cancer. MATERIALS AND METHODS This retrospective analysis included a total of 99 patients who had invasive breast cancer and were treated surgically between January 2012 and July 2013. The expression of phosphorylated ribosomal protein S6-kinase-1 (p-S6K1), phosphorylated protein kinase B (p-AKT), and estrogen receptor (ER) were assessed immunohistochemically on both CNBS and SS for each patient. RESULTS The expression rate of phosphoprotein at any intensity was higher on CNBS than on SS (p-S6K1, 99.0% versus 59.6%; p-AKT, 94.9% versus 56.6%). p-S6K1and p-AKT expression was classified as negativity (absence to weak staining) or positivity (moderate to strong staining) for further analysis. For p-S6K1, 24.2% of patients showed positivity on CNBS and negativity on SS, while 7% of the patients showed negativity on CNBS and positivity on SS. For p-AKT, 70.7% of the patients showed positivity on CNBS and negativity on SS, while only 1.0% of patients showed negativity on CNBS and positivity on SS. CONCLUSION CNBS may be the more appropriate specimen type for immunohistochemical examination of phosphoprotein expression in invasive breast cancer.