The purposes of this study were to determine the prevalence of malocclusion among children with autism spectrum disorder (ASD) and to describe the most common malocclusion traits in this population. This cross-sectional study included patients diagnosed with ASD aged between 5 and 18 years. Randomly selected healthy children with the same demographic characteristics comprised the control group. Dental charts were reviewed to obtain the children's sociodemographic characteristics and type of occlusion. Information on each child's molar occlusion classification (Angle classification), midline deviation, crossbite, open bite, overbite, overjet, and crowding were recorded. The statistical analysis used descriptive analysis, the Pearson chi-square test, and multivariate logistic regression. Ninety-nine children comprised the ASD group, and 101 children were in the control group. Our results demonstrated a significantly higher prevalence of malocclusion in children with ASD compared with the control group (P <0.001). Patients with ASD were significantly more likely to have posterior crossbite (P = 0.03), increased overjet (P <0.0001), and severe maxillary crowding (P <0.01). Furthermore, children with ASD were more likely to have malocclusion than non-ASD children, independently of their demographic characteristics (odds ratio, 2.6; 95% confidence interval, 1.46, −4.65). The prevalence of malocclusion was higher among children with ASD. Posterior crossbite, increased overjet, and severe maxillary crowding were the most common malocclusion traits in these children. •Children with autism have a higher prevalence of malocclusion compared with controls.•Posterior crossbite, abnormal overjet, and maxillary crowding are the most common traits.•Better understanding of malocclusion patterns could be useful.