Amelogenesis imperfecta (AI) is a disease in which there is a defect in the formation of the tooth enamel of deciduous and permanent teeth. In an attempt to clarify the genetic abnormality in patients with amelogenesis imperfecta, we have been investigating their amelogenin gene. In this study, we have determined the nucleotide sequences of regions of the intron 1 and intron 2 of the X and Y human amelogenin genes (AMGX, AMGY) for the first time, and established a polymerase chain reaction (PCR) protocol to amplify six exons of AMGX and AMGY for the diagnosis of amelogenesis imperfecta, because previous studies have shown that some of the AI patients have such mutations. This study gives us an easy and fast method to analyze protein encoding regions of the amelogenin genes. The applications of this method will give us better insight into classifying AI, followed by understanding of the cause of the disease.