Objective: The purpose of this study is to compare the computer-assisted planimetry and point-counting methods in evaluating the sizes of the mandibular cysts with respect to their agreement and the time required to analyze. Study Design: The surface areas of 46 mandibular cyst lesions on orthopantomograms were estimated using the point-counting and computer-assisted planimetry methods. Three observers evaluated the outlined areas twice, using the point-counting (PC) and computer-assisted planimetry (CAP) methods with an interval of two weeks. In the planimetry technique, digitalized images and ImageJ software were used to measure the surface area of the half mandibles and cysts. The grids were superimposed over the same images and the number of points hitting the interested structures was counted for the point-counting technique. The projection area fraction (PAF) of the cysts within the mandible was estimated using the obtained values by means of the two techniques. Intraclass correlation coefficient was used to assess the level of agreement between the two methods. Inter-rater reliability analysis using the Kappa statistic was performed to determine consistency among raters. Results: CAP and PC techniques showed consistent intra-observer values in all observers. Intraclass correlation between CAP and PC measurements of first, second and third observers were found to be 0.9986, 0.9988 and 0.9994 respectively. The durations of PC technique was 32% higher than the CAP technique. Conclusion: PC and CAP methods were seemed to show sufficient agreement to be used interchangeably. The main disadvantage of the PC analysis is it takes more time than CAP method.