Tumours arising from oral minor salivary glands may exhibit an overlap of clinical and morphological features that may produce diagnostic and therapeutic dilemmas. The aim of this study is to asses the value of fine needle aspiration cytology (FNAC) in differentiation of benign and malignant tumours and to render a specific diagnosis. We evaluated the team work of surgeon and cytologist to improve diagnostic accuracy. Two steps are important for accuracy: sampling aspirate that should be done together by surgeon and cytologist and cytological microscopic analysis of the smears that should be performed by an experienced cytologist. The study included 132 patients with intraoral minor salivary gland tumours between 2002 and 2011. Adequate material was obtained from 121 (91.7%) patients. FNAC was usually performed by cytologist in a team with maxillofacial surgeon at cytology department that is more convenient for preparing the samples and especially for ROSE procedure (rapid-on site evaluation) of smears. In such a way the cytologist checked the adequacy of samples and decided whether some ancillary techniques should be used and therefore repeat FNAC. A total of 82 patients underwent surgery, 40 with malignant and 42 with benign tumours. Preoperative cytological diagnoses were compared with histopathological ones using histopathology as a gold standard. The most common benign tumour was pleomorphic adenoma and among malignant tumours adenoid cystic carcinoma. The most commonly affected site was the palate. The team work of surgeon and cytologist achieved specificity of 95.1%, sensitivity of 97.6% and diagnostic accuracy of 96.3%. We can conclude that although subclassification of some tumour types of salivary glands remains poor, FNAC is invaluable in patient triage and therefore should be considered in the first line investigations of these lesions by the cytologist and surgeon.