INTRODUCTION: The aim of this study was to compare the pattern and prevalence of associated dental anomalies between maxillary and mandibular tooth agenesis (hypodontia). METHODS: A sample of 3315 dental patients, aged 8.6 to 25.4 years, was surveyed for tooth agenesis (excluding third molars): 106 subjects were diagnosed with maxillary hypodontia (group 1) and 70 with mandibular hypodontia (group 2). Both groups were examined for the following dental anomalies: retained deciduous molars, infraocclusion of deciduous molars, impaction, microdontia of maxillary lateral incisors, supernumerary teeth, transposition, transmigration, and ectopic eruption of the permanent molars. For statistical testing, the chi-square test (P <0.05) was used to compare the occurrences of these anomalies among the groups. RESULTS: We found that 77.5% of the patients in the mandibular hypodontia group had at least 1 dental anomaly compared with 49.5% in the maxillary hypodontia group (P <0.0001). The only dental anomaly with a significantly increased prevalence in the maxillary hypodontia group compared with the mandibular hypodontia group was microdontia of the maxillary lateral incisors (groups 1, 46.7%; group 2, 12.9%; P <0.0001). On the other hand, the prevalences of retained deciduous molars (group 1, 9.4%; group 2, 60.0%), infraoccluded deciduous molars (group 1, 0.9%; group 2, 7.1%), and impacted teeth (group 1, 22.6%; group 2, 38.6%) were significantly higher in the mandibular hypodontia group. The prevalences of supernumerary teeth, transposition, transmigration, and ectopic eruption of permanent molars were low and not significantly different between the groups. CONCLUSIONS: Tooth agenesis isolated to the maxilla is frequently associated with microdontia of the maxillary lateral incisors, whereas tooth agenesis isolated to the mandible is frequently associated with retained deciduous molars, infraoccluded deciduous molars, and impacted teeth. The results of this study may provide additional evidence supporting the field-specific genetic control theory for dental development in both jaws.