INTRODUCTION: The purposes of this study were to investigate the patterns of tooth agenesis (oligodontia and nonoligodontia), maxillary canine impaction, and tooth transposition in subjects with Down syndrome and to determine whether congenital heart disease and hypothyroidism are parameters in tooth agenesis. METHODS: The study included 114 patients with Down syndrome. The data were quantified by using standardized records, clinical examinations, panoramic radiographs, and solo roentgenograms. The subjects were differentiated into oligodontia (6 or more teeth missing) and nonoligodontia (5 or fewer teeth missing). RESULTS: In these patients with Down syndrome, 59.6% had missing teeth. Those in the nonoligodontia group showed a tendency toward a negative correlation between congenital heart disease and agenesis (P = 0.093; odds ratio = 0.49) but a slight positive correlation between hypothyroidism and agenesis (P = 0.060; odds ratio = 3.71). In the oligodontia group, there was a quantitatively and qualitatively different pattern, indicating another phenotype. When both mandibular central incisors were missing, there was a remarkable chance for oligodontia (P = 0.001; odds ratio = 38.8). In the mandible, symmetrical agenesis of the canines and lateral incisors was more frequent in the nonoligodontia group. CONCLUSIONS: The oligodontia (with a different phenotype) and nonoligodontia groups had different patterns of agenesis. Maxillary canine impaction was not related to absence of the lateral incisors. Absence of both mandibular central incisors was a high predictor for oligodontia. Congenital heart disease and hypothyroidism are parameters involved in tooth agenesis.