Background and Aims: Temporomandibular disorder (TMD) is a common problem in maxillofacial area, which is often diagnosed with pain, temporomandibular joint malfunction and masticatory muscles dysfunction. Teenagers and adolescents are susceptible to TMD, but no information is available regarding the prevalence of TMD in this groups. Furthermore, a few investigations have evaluated the prevalence of TMD in mixed dentition. The aim of this study was to evaluate the prevalence of TMD in mixed dentition and its association with malocclusion.Materials and Methods: In this cross-sectional study, 222 patients with the age of 6-12 years referred to Pediatric and Orthodontic departments of Tehran University Dental School were evaluated. Clinical examinations were done and questionnaires were filled out. The data were analyzed using SPSS 11.5 and logistic regression test.Results: The prevalence of TMD in mixed dentition was 14.4%, which was higher in girls compared with the boys. The most TMD prevalence in the mixed dentition was seen in 11-12 year old patients. The prevalence of joint sound, masticatory muscle tenderness, and joint pain was 23.9%, 20.9%, and 5.4%, respectively. CL III malocclusion showed higher TMD prevalence and also TMD was more common in children with 6 mm overjet and more. Unilateral posterior cross bite, deviation of mandible, and TMD were significantly related to each other.Conclusion: In the present study, temporomandibular disorder was related to malocclusion.