Background <p>Assessment of the effect of segmentation technique (manual Vs semiautomatic) on the accuracy of linear measurements of the CBCT reconstructed 3D mandibular condyle compared to the real measurements of the actual condyle.</p> Materials and methods <p>fifteen dry mandibular with 30 condyles were included in this study, where condylar real linear measurements (L1, L2&amp; L3) were assessed using a digital caliper. Then each mandible was assembled to a skull in a normally closed TMJ position, this assembly was scanned using Planmeca Promax 3D Mid CBCT machine with a standard imaging protocol. Later, <i>3D Slicer</i> open-source segmentation software was used for manual and semiautomatic segmentation of mandibular condyles from the CBCT images. Afterward, the same linear measurements were assessed again on the CBCT reconstructed 3D condyles. Statistical analysis showed a normal distribution of the numerical data of all linear measurements, so repeated measures ANOVA followed by Bonferroni post hoc test were used to compare the measurements on the 3D segmented CBCT condyles to their corresponding real measurements. Reliability analysis using the intraclass correlation coefficient (ICC) test was also adopted.</p> Results <p>There was no statistically significant difference in linear measurement errors between manually and semiautomatically segmented condyles. The manual and semiautomatic segmented condylar width(L1) measurements showed excellent agreement with real measurements, while length (L2) measurements showed good agreement, and height (L3) measurements had poor agreement.</p> Conclusion <p>We're using the Semiautomatic segmentation technique provides a reliable and time-saving segmentation approach that can yield accurate results compared to manual segmentation.</p> Trial registration <p>The study protocol was registered on <a href="http://www.clinicaltrials.gov">www.clinicaltrials.gov</a> (ID: NCT05435417).</p>