Odontogenic cysts are a diverse group of pathologic entities with different proliferation potential, leading to variations in their biological behavior. One of the most cited proliferation markers used in diagnostic histopathology is Ki-67. Another group of proteins recently investigated is minichromosome maintenance (MCM-3) and its expression has been evaluated in several odontogenic lesions but the results were controversial. Thus, the present study endeavored to compare the expression of MCM-3 and Ki-67 in odontogenic cysts. Furthermore, a pioneer attempt was made to evaluate the sensitivity of these markers to inflammation. A total of 101 cases (37 dentigerous cysts, 37 odontogenic keratocysts, and 27 radicular cysts) were included. Immunohistochemical expression of Ki-67 and MCM-3 were investigated using a labeling index (LI). In addition, they were scored for inflammation, followed by correlation with both markers. The data obtained were subjected to statistical analysis (P<0.05). Overall, a higher LI of MCM-3 than Ki-67 was obtained in all study groups along with a positive correlation of Ki-67 LI with inflammation. Thus, MCM-3 proteins proved to be a more accurate means to determine the proliferation potential and were not sensitive to external stimuli like inflammation than conventional markers, such as Ki-67.