This study was carried out to determine the prevalence of temporomandibular joint (TMJ) dysfunction in mixed and permanent dentition and to evaluate the sex distribution in Turkish children. One hundred and eighty-two children with mixed dentition and 212 with permanent dentition were selected for the study, which used a questionnaire and clinical examination. Children with one or more signs (TMJ sounds, TMJ tenderness, muscle tenderness, restricted mouth opening) and/or symptoms (TMJ pain during mastication and mouth opening, restriction of the jaw opening and TMJ sounds) met the criterion of TMJ dysfunction. The total prevalence of signs and symptoms of TMJ dysfunction in the studied population was 68% (68% in girls and 68% in boys) in mixed dentition and 58% (61% in girls and 56% in boys) in permanent dentition. The Z-test and analysis of variance (ANOVA) were used for statistical analysis of the difference between the results. The total prevalence of signs and symptoms of TMJ dysfunction in mixed dentition was found to be higher than in permanent dentition (P < 0.05). No statistically significant difference was found in the total prevalence of TMJ dysfunction between girls and boys.