To compare the characteristics of mandibular asymmetry in patients with unilateral craniofacial microsomia (CFM) and class II asymmetry. Pretreatment cone-beam computed tomography of consecutive adults with Pruzansky-Kaban type I and IIA CFM (CFM group) was analyzed by 3D cephalometry. Fourteen mandibular landmarks and two dental landmarks were identified. The mandibular size and positional asymmetry were calculated by using landmark-based linear and volumetric measurements, in terms of asymmetry ratios (affected/non-affected side) and absolute differences (affected - non-affected side). Results were compared with non-syndromic class II with matched severity of chin deviation (Class II group). Statistical analyses included independent t test, paired t test, chi-square test, and ANOVA. CFM group (n, 21; mean age, 20.4 +- 2.5 years) showed significantly larger size asymmetry in regions of mandibular body, ramus, and condyle compared to Class II group (n, 21; mean age, 27.8 +- 5.9 years) (p < 0.05). The curvature of mandibular body was asymmetric in CFM. Regarding the positional asymmetry of mandibular body, while a comparable transverse shift and a negligible yaw rotation were found among the two groups, the roll rotation in CFM was significantly greater as well as the occlusal (6.06deg vs. 4.17deg) and mandibular (7.84deg vs. 2.80deg) plane cants (p < 0.05). Mild CFM showed significantly more severe size asymmetry and roll rotation in mandible than non-CFM class II asymmetry. To improve the mandibular size and positional asymmetry in CFM, adjunct hard tissue augmentation or reduction in addition to OGS orthodontics with a meticulous roll and yaw planning is compulsory, which is expected to be distinct from treating non-CFM class II asymmetry.