Quantification of skeletal symmetry in a healthy population could have a strong impact on the reconstructive surgical procedures where mirroring of the contralateral healthy side acts as a clinical reference for the restoration of unilateral defects. Hence, the aim of this study was to three-dimensionally assess the symmetry of skeletal midfacial complex in skeletal class I patients. A sample of 100 cone beam computed tomography (CBCT) scans (50 males, 50 females; age range: 19-40years) were recruited. Automated segmentation of the skeletal midfacial complex was performed to create a three-dimensional (3D) virtual model using a convolutional neural network (CNN)-based segmentation tool. Thereafter, the segmented model was mirrored and registered to quantify skeletal symmetry using a color-coded conformance mapping based on a surface part comparison analysis. Overall, the mean and root-mean-square (RMS) differences between complete true and mirrored models were 0.14 ± 0.12 and 0.87 ± 0.21mm, respectively. Female patients had a significantly more symmetrical midfacial complex (mean difference: 0.11 ± 0.1mm, RMS: 0.81 ± 0.17mm) compared to male patients (mean difference: 0.16 ± 0.13mm, RMS: 0.94 ± 0.23mm). No significant difference existed between left and right sides irrespective of the patient's gender. The comparison between true and mirrored complete and left/right split midfacial complex showed symmetry within a clinically acceptable range of 1mm, which justifies the applicability of using the mirroring technique. The presented data could act as a reference guide for surgeons during planning of reconstructive surgical procedures and outcome assessment at follow-up.