Objective: The exact volume of the bone cyst is fundamental for evaluation, treatment, and surgical management of the pathology related to any bone. The aim of this study was to introduce the stereological point-counting technique in bone cyst volume measurements on computed tomography images and to compare it with the planimetry technique. Methods: A total of 30 bone cyst volumes were estimated on CT images using stereological point-counting and the planimetry technique, which is based on the Cavalieri principle. The planimetric measurements were regarded as reference values. The stereological and planimetric volume estimations were performed by two independent observers twice. The estimation results of the two volumetric techniques were compared with the Wilcoxon signed-rank test. Intra-observer and inter-observer reliability of each volumetric technique was assessed. Results: For each bone cyst, 7-11 systematically sampled CT slices enabled reliable cyst volume estimations with a low coefficient of error (0.39%-3.12%). There was no significant difference between point counting and planimetry methods regarding volume measurements in both sessions (p>0.05), and these methods correlated well with each other. There was a significant inter-and intra-observer agreement for each volumetric method (ICC=0.9984 to 0.9988). The stereological approach was observed to take less time than the planimetric approach (mean 01:43±0.44 vs. 03.33±1:47 minutes) Conclusion: The stereological point-counting method can be well pertained to CT images for the reliable and reproducible assessment of bone cyst volume. Application of the point-counting method for volume estimation of bone cysts with different morphological features provides a great advantage in terms of both time-saving, applicability, and practicality in comparison with the planimetry technique. Keywords: Bone cyst, computed tomography, planimetry, stereology, volume measurement