The aim of this study was to investigate the value of 3D Statistical Shape Modelling for orthognathic surgery planning. The goal was to objectify shape variations in the orthognathic population and differences between male and female patients by means of a statistical shape modelling method. Pre-operative CBCT scans of patients for whom 3D Virtual Surgical Plans (3D VSP) were developed at the University Medical Center Groningen between 2019 and 2020 were included. Automatic segmentation algorithms were used to create 3D models of the mandibles, and the statistical shape model was built through principal component analysis. Unpairedt-tests were performed to compare the principal components of the male and female models. A total of 194 patients (130 females and 64 males) were included. The mandibular shape could be visually described by the first five principal components: (1) The height of the mandibular ramus and condyles, (2) the variation in the gonial angle of the mandible, (3) the width of the ramus and the anterior/posterior projection of the chin, (4) the lateral projection of the mandible’s angle, and (5) the lateral slope of the ramus and the inter-condylar distance. The statistical test showed significant differences between male and female mandibular shapes in 10 principal components. This study demonstrates the feasibility of using statistical shape modelling to inform physicians about mandible shape variations and relevant differences between male and female mandibles. The information obtained from this study could be used to quantify masculine and feminine mandibular shape aspects and to improve surgical planning for mandibular shape manipulations.