Significant facial asymmetry can lead to both functional and aesthetic issues. Often, such asymmetry originates from irregularities in the jaw structure. It is critical to recognize that asymmetries can be concealed by soft tissue, which may be overlooked. The aim of this study is to investigate the relationships between bilateral landmarks in the vertical dimension of facial asymmetry among individuals with skeletal Class II and Class III malocclusions. Fifty-two adult patients with a mean age of 24.4 ± 3.79 years with facial asymmetry who underwent orthodontic and orthognathic surgery were studied. Cone-beam computed tomography and facial scans were used to create 3D virtual head models which enhanced the accuracy in addressing facial asymmetry to ensure effective treatment planning. Each landmark was measured and digitized using the Dolphin Imaging program. The findings showed a correlation between gender and type of skeletal discrepancies with the menton deviation direction. In conclusion, the vertical discrepancy between bilateral landmarks was observable in both hard and soft tissues with more pronounced expression in soft tissues. This discrepancy was characterized by an elevation on the same side as the menton deviation, which was a feature observed in both skeletal Class II and Class III individuals.