It is well established that estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor (HER2) could be regarded as prognostic factors in breast cancer. Ultrasound-guided fine needle aspiration cytology (FNAC) has revolutionized the management of cancers, providing less invasive and quick diagnostic method. There are hardly any studies on the correlation between cytomorphology and prognostic biomarkers. We retrospectively analyzed the immunohistochemistry and the fluorescence in situ hybridization of breast cancer specimens from 252 patients, who have been diagnosed as breast cancer at our hospital. Morphological features of cytology smears were scored. The relationship between cytological features and three biomarkers were analyzed. Based on this, we developed a system to predict the status of biomarkers. The results indicated that some cytological parameters, especially the features of nucleoli, were distinctively related to the makers' expression. In the novel scoring system, a cutoff of 12.0 provided a statistical discrimination for cytological grading. We concluded that cytomorphological features were associated with prognostic factors. The HR+ neoplasms showed scattered micronucleoli, while HER2+ neoplasms demonstrated centered macronucleoli. We summarized a scoring system to predict the status of three factors. This may help us to broaden the application of breast cancer cytology.Copyright © 2022 Yunzhu Li et al.