Purpose: This study was performed to evaluate the effect of voxel size on the accuracy of landmark identification in cone-beam computed tomography (CBCT) images. Materials and Methods: CBCT images were obtained from 15 dry human skulls with two different voxel sizes; 0.39 mm and 0.10 mm. Three midline landmarks and eight bilateral landmarks were identified by 5 examiners and were recorded as three-dimensional coordinates. In order to compare the accuracy of landmark identification between large and small voxel size images, the difference between best estimate (average value of 5 examiners’ measurements) and each examiner’s value were calculated and compared between the two images. Result: Landmark identification errors showed a high variability according to the landmarks in case of large voxel size images. The small voxel size images showed small errors in all landmarks. The landmark identification errors were smaller for all landmarks in the small voxel size images than in the large voxel size images. Conclusion: The results of the present study indicate that landmark identification errors could be reduced by using smaller voxel size scan in CBCT images.