The purpose of this retrospective study was to assess the prevalence and distribution of hypodontia in the permanent dentition, excluding the third molars, in a sample of Japanese orthodontic patients. Orthopantomograms of 3358 Japanese orthodontic patients (1453 boys and 1905 girls) between the ages of 5 and 15 years were examined for evidence of hypodontia. The prevalence of hypodontia was 8.5% (7.5% for boys, 9.3% for girls) with no statistically significant difference between the sexes. The average number of missing teeth per child was 2.4 (2.5 for boys, 2.4 for girls). Most (76.3%) children with hypodontia were missing either 1 or 2 teeth (77.1% for boys, 75.7% for girls). The prevalence of advanced hypodontia was 10.1% (11.0% for boys, 9.7% for girls). The most commonly missing teeth were the mandibular second premolars, followed by the mandibular and maxillary lateral incisors, and the maxillary second premolars; minor differences in the order of prevalence existed among groups of children classified by the number of missing teeth. Symmetrical hypodontia was predominant, and the most commonly symmetrical hypodontia was mandibular second premolar agenesis. No consistent finding was obtained as to which jaw had more missing teeth. The distribution of missing teeth was similar between the right and left sides of the dental arches in each group of children. Anterior tooth agenesis was predominant in children with minor hypodontia, and posterior tooth agenesis increased with hypodontia severity. The distinct characteristic of hypodontia in the Japanese population compared with other populations was a higher prevalence of both advanced hypodontia and mandibular lateral incisor agenesis in children with minor hypodontia.