The aim of this study was to determine the correlation between congenitally missing third molar tooth germs and sagittal maxillomandibular jaw dimensions in orthodontic patients in Japan. The subjects were 391 patients from the orthodontic clinic of the Hokkaido University Dental Hospital who were less than 15 years of age. Assessments were made from panoramic radiographs and lateral cephalograms. The subjects were divided into a maxillary/mandibular third molar absent and an existent group. The ANB angle and the sagittal dimensions of the nasal floor (ANS-PNS), maxillary basal bone (Mx), mandibular corpus (Go-Pog), and mandibular basal bone (Mn) were measured. Logistic regression analysis was used to estimate associations between third molar agenesis and these measures. The following results were obtained: (1) The frequency of the maxillary third molar agenesis significantly increased with decreasing Mx (odds ratio = 0.559, 95% confidence interval = 0.377 - 0.829). The frequency of the mandibular third molar agenesis also increased with decreasing Mx (odds ratio = 0.532, 95% confidence interval = 0.330 - 0.856). (2) There were no significant correlations between Mn and mandibular third molar agenesis. These results suggest that agenesis of third molar germs does not depend on anteroposterior dimensions of the mandible but depends on anteroposterior dimensions of the maxilla in Japanese orthodontic patients.