Background Fine‐needle aspiration cytology (FNAC) is a noninvasive, safe, cost‐effective, diagnostic procedure for the evaluation of salivary gland lesions and the selection of patients for surgery. The aim of this study was to analyze the risk of malignancy (ROM) according to the Milan reporting system of salivary gland FNA specimens using a liquid‐based cytology (LBC) technique. Methods The cytological diagnosis of 459 cases between 2014 and 2017 was revised according to the Milan reporting system. The FNAC results of 129 cases with a histological diagnosis were compared with respect to the final diagnosis. The ROM for each category calculated. Results The ROM was high in the indeterminate and malignant categories, while the ROM in the benign neoplasm category was low. Sensitivity and specificity analyzed in two different ways were 95.1% and 88.8%, 81%, and 77.7%, respectively. Conclusions When salivary gland lesions are evaluated together with clinical and radiological data, the LBC technique can be applied to salivary gland specimens based on the high diagnostic sensitivity and specificity in liquid‐based samples reported according to the Milan system.