Background: Successful removal of salivary stones depends on exact pretreatment information of the location, the size and shape of the stones. This study aimed to compare the volume of submandibular sialoliths determined by preoperative Cone-Beam Computer Tomography (CBCT) scans with the volume of the removed stones on micro-Computer Tomography (micro-CT) scans. Material and Methods: In this study, using twenty-one submandibular sialoliths, the pretreatment volumes in-vivo measured on CBCT were compared to the volumes of removed stones determined by micro-CT scans. The volume measured on micro-CT scans served as the gold standard. Pre-operative CBCT’s and in-vitro micro-CT’s were converted into standard tessellation language models (STL-models) using an image segmentation software pack-age. The CBCT and micro-CT images of the stones were subsequently metrologically assessed and compared to each other using reverse engineering software. Results: Volumes of submandibular sialoliths determined by CBCT’s correlated significantly with volumes measured on micro-CT’s (Spearman’s coefficient r = 0.916). The interquartile range (IQR) for the volume measured with micro-CT was 117.23. The median is 26.41. For the volume measured with CBCT the IQR was 141.3 and the median 36.61. The average volume on micro-CT is smaller than on CBCT. Conclusions: When using CBCT-scans for the detection of submandibular sialoliths one should realize that in-vivo those stones are actually a fraction smaller than assessed on the preoperative scan. This is important when cut-off values of sizes of stones are used in the pretreatment planning of stone removal.