Background: Proliferation markers widely have been used to diagnose and determine the behaviour and prognosis of benign and malignant tumours. Minichromosome maintenance 3 (MCM3) is a novel proliferation marker. The aim of this study was to evaluate and compare MCM3 with Ki-67 in diagnosis of salivary gland tumours. Materials and Methods: In this retrospective study, immunohistochemical expression of MCM3 and Ki-67 was evaluated in 15 pleomorphic adenomas (PA), 17 mucoepidermoid carcinomas (MEC) and 18 adenoid cystic carcinomas (ADCC). Labeling indices (LIs) for the two markers were calculated and compared. Results: MCM3 and Ki-67 LIs were significantly higher in MEC and ADCC compared to PA. The LI of MCM3 was significantly higher than that of Ki-67 in MEC and PA. There was no significant difference between the two markers in ADCC. A cut-off point of 8% with 74.3% sensitivity and 93.3% specificity for MCM3 was obtained to discern between benign and malignant tumors. Conclusions: These results suggest that MCM3 might be a useful proliferation marker for differential diagnosis and recognition of clinical behavior of salivary gland tumors.