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Background: The diagnostic accuracy of fine needle aspiration cytology (FNAC) of salivary lesions is relatively high, but cytologic interpretation might be confusing if the sample is lacking typical cytologic features. Methods: There were 77 cases of benign salivary lesions, consisting of pleomorphic adenoma (PA) in 61 cases, Warthin’s tumor (WT) in 12 cases, and other benign lesions in 4 cases. The causes of the discrepancies between the FNAC and the histologic diagnoses were evaluated. Results: Major discrepancies were noted in 4 of the 61 PA cases, and in 1 of 12 WT cases. The causes of the major discrepancies were a mislabeled site in 1 PA and 1 WT case, and an interpretation error in 3 PA cases. Minor discrepancies were more common in the WT cases (7 of 12 cases) than in the PA cases (11 of 61 cases). The causes of the minor discrepancies were a mislabeled site in 1 PA and 1 WT case, an inadequate sample in 7 PA and 2 WT cases, a lack of typical cytomorphology in 2 PA and 2 WT cases, and an interpretation error in 1 PA and 2 WT cases. Conclusions: To increase the diagnostic accuracy in the benign salivary lesions, recognition of both characteristic and less typical cytomorphology is needed.