OBJECTIVE: To determine the prevalence of hypodontia in the general population and orthodontic population in adolescent Chinese Hans. METHODS: Two groups named the general population (6015 subjects) and the orthodontic population (2781 subjects) were investigated, respectively. The former came from the students of three general universities in North China and the latter came from patients coming to the Department of Orthodontics, Peking University School and Hospital of Stomatology for orthodontic consulting during the summer and winter holidays in 2008. The prevalence and average missing number of hypodontic teeth was investigated in the two groups. The distribution of missing teeth was analysed between jaw positions and between genders. RESULTS: The prevalence of tooth agenesis was found to be 5.89% for the general population group and 7.48% for orthodontic subjects. Tooth agenesis was more frequently found in females than in males in both of the two groups and showed a statistically significant difference (P < 0.01). Tooth agenesis was found more frequently in the mandible than in the maxilla in the general population but had no difference in the orthodontic population. The prevalence and the number of missing teeth were higher in the orthodontic population than in the general population. Tooth agenesis showed different characteristics in the two populations. The congenital absence of the second mandibular premolars and the maxillary lateral incisors increased in the orthodontic population. Gender difference in hypodontia expressed an opposite effect in the two groups. Although tooth agenesis was more frequently found in females than in males, males missed more teeth than females in the orthodontic population. CONCLUSION: Tooth agenesis showed different characteristics between the general and orthodontic adolescent Chinese populations.