The synthesis of tooth development biology with human studies focusing on inherited conditions that specifically interfere with tooth development is improving our understanding of normal and pathological tooth formation. The type of inherited dental malformations observed in a given kindred relate to when, during odontogenesis, the defective gene is critically expressed. Information about the protein encoded by the defective gene and the resulting dental phenotype helps us understand the major processes underway at different stages during tooth development. Genes affecting early tooth development (PAX9, MSX1, and AXIN2) are associated with familial tooth agenesis or oligodontia. Genes expressed by odontoblasts (COL1A1, COL1A2, and DSPP), and ameloblasts (AMELX, ENAM, MMP20, and KLK4) during the crown formation stage, are associated with dentinogenesis imperfecta, dentin dysplasia, and amelogenesis imperfecta. Late genes expressed during root formation (ALPL and DLX3) are associated with cementum agenesis (hypophosphatasia) and taurodontism. Understanding the relationships between normal tooth development and the dental pathologies associated with inherited diseases improves our ability to diagnose and treat patients suffering the manifestations of inherited dental disorders.