The identification of specific patterns of dental anomalies would allow testing the hypothesis that certain genetic and environmental factors contribute to distinct dental anomaly subphenotypes. A sexual dimorphism in tooth agenesis and its association with other dental anomalies has been suggested. The aim of this study was to investigate a large group of children to define dental anomaly subphenotypes that may aid future genetic studies. Orthopantamograms of 1198 subjects were examined and 1167 were used in this study. The frequency of tooth agenesis in the studied population was 4.8%. Male:female ratios varied from 2:1 in the agenesis of upper lateral incisors to 0.5:1 in premolar agenesis. The risk of infra-occlusion of primary molars and double formation of primary incisors was increased in individuals with tooth agenesis.