The aim of this retrospective study was to identify general health problems as potential predisposing factors for hypodontia in a population of Japanese orthodontic patients. The study included 3683 individuals (1312 males and 2371 females, 13-42 years of age; mean, 23 years 7 months). Dental pantomograms (DPTs) were used to diagnose hypodontia. Health histories were obtained through a questionnaire administered by the dentist in charge. The Mantel-Haenszel test was used to determine the significance of the differences in the prevalence of health problems. The overall frequency of hypodontia was 5.8 per cent. The average number of missing teeth per patient was 1.7. There was a high prevalence of systemic complications, which included allergy, asthma, atopy, and enlarged adenoids associated with hypodontia. Only allergy showed a significant relationship with hypodontia (P < 0.01). The environmental aetiology of hypodontia is not yet fully understood. However, based on the results of this retrospective study, predisposing general health problems, especially allergy, seem to be involved.