To analyze the correlation between the phenotype and genotype of tooth agenesis using the tooth agenesis code (TAC) and the traditional descriptor for missing teeth.Patients with isolated hypodontia caused by PAX9 or MSX1 mutation reported before May 2007 were enrolled. The teeth missing rate and TAC code were recorded. The missing teeth patterns caused by the two mutations were compared.The teeth missing rates in each teeth positions were significantly different between maxillary and mandibular except maxillary central incisor, lateral incisor and mandibular canine, first molar (P<0.05, P<0.001). MSX1 gene mutation often led to the loss of maxillary first premolar, maxillary second premolar, and mandibular second premolar, while PAX9 gene mutation often led to the loss of the first, second, and third molars. The results were similar when analyzed either by TAC code analysis or by traditional descriptor.PAX9 and MSX1 gene mutation can cause different phenotypes of tooth agenesis. The TAC code can be used in the analysis of the correlation between phenotype and genotype of the missing teeth patients.