Tooth development is regulated by a reciprocal series of epithelial-mesenchymal interactions. With the large number of genes involved in the odontogenesis process, the opportunity for mutations to disrupt this process is high. Mutational analysis has revealed genes that are major causes of non-syndromic hypodontia. The most common permanent missing teeth are the third molars, second premolars, and maxillary lateral incisors. Although hypodontia does not represent a serious public health problem, it may cause masticatory and speech dysfunctions and esthetic problems. Msx1 (Muscle Segment Box) is believed to play an important role in tooth development. To further investigate the role of the gene in human hypodontia, we analyzed genotypes in a family with hypodontia using the SSCP assay. Examinations of all affected and unaffected members of the family studied indicated that 5 of the 10 family members had hypodontia, and it was possible to observe polymorphisms/mutation by SSCP as bands with an anomalous migration pattern in individuals with hypodontia. Our data suggest that Msx1 gene polymorphism is associated with hypodontia.