Estrogen receptor (ER) and progesterone receptor (PR) overexpression can be used to predict patient prognosis in breast cancer (BC). Human epidermal growth factor receptor 2 (HER2) is a reliable predictive marker in invasive breast cancer (IBC). Thin-Prep (TP) specimens are commonly utilized for immunocytochemistry (ICC) in fine needle aspiration cytology (FNAC). Thus, we sought to investigate if the incorporation of molecular diagnosis performed on TP-processed specimens is applicable in clinical practice.Hormone receptors (HRs) and HER2 immunocytochemistry was performed on 542 primary breast cancer FNAC specimens using the TP method. One hundred fourteen HER2 fluorescence in situ hybridization (FISH) analyses were performed on HER2 ICC 2+ FNAC specimens and the corresponding tissue samples. HRs results of TP slides and those of formalin-fixed paraffin-embedded (FFPE) slides were correlated well for ER (concordance rate = 93.3%, kappa value = 0.85) and PR (concordance rate = 88.6%, kappa value = 0.75). HER2 results for the TP slides and those of the matched FFPE slides also correlated well (concordance rate = 80.0%, kappa value = 0.62). The specificity of HER2 was 97.3%; however, the sensitivity was only 67.1%. Cytological specimens and histological samples showed a strong correlation (concordance rate = 99.1%, kappa value = 0.98) while being used to evaluate HER2 gene amplification.FNAC is a minimally invasive technique that can be used as an alternative method to collect tissue especially in cases where an excisional or core biopsy is difficult to obtain, or when recurrence is present. The results of ICC HRs in FNAC TP specimens may be used instead, but HER2 assessment may not be reliable enough for clinical use. FISH testing is necessary in this setting.