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Background: The diagnostic performance of cytology was compared with the frozen results and its usability was evaluated as a rapid diagnosis method in intraoperative thoracic surgery in a single institution (Istanbul, Turkey).Methods: All 197 subsequent patient specimens (cases) from 158 patients who were sent to our department from the thoracic surgery clinic for an intraoperative diagnosis request between the years 2016 and 2021 were evaluated. Obtained results from frozen and cytology were compared with final paraffin section diagnoses. Lesions were grouped into three different groups as nonneoplastic, benign, and malignant neoplasms.Results: Diagnostic accuracy values of cytology and frozen sections in intraoperative consultation were 98.8% and 99.4%, respectively. Sensitivity values of cytology and frozen sections in intraoperative consultation were 96.3% and 98.7%, respectively. Specificity values of cytology and frozen sections in intraoperative consultation were 100% and 100%, respectively. Negative predictive values of cytology and frozen sections in intraoperative consultation were 96.7% and 98.9%, respectively. Positive predictive values of cytology and frozen sections in intraoperative consultation were 100% and 100%, respectively. Kappa statistics between cytology and frozen revealed a very high interrater reliability (Cohen's Kappa value: 0.911; p = .001; p < .01). The difficulty in distinguishing primary and metastatic carcinoma, which is mostly undecided in frozen sections and the definitive diagnosis is left to paraffin sections, seems also be a problem in the cytological examination.Conclusions: Cytological diagnosis can be used in the evaluation of small biopsy specimens that require tissue preservation in intraoperative consultation, especially for immunohistochemical and advanced genetic studies.