Tooth agenesis constitutes one of the most common developmental anomalies in man. Oligodontia is defined as congenital absence of six or more teeth. Based on the studies of our team in cooperation with Peking University Center for Human Disease Genomics in the past five years, this article reviews the current research progress in clinical phenotypes and case collection, epidemiological investigation and etiological genetic studies of oligodontia. The symptoms of oligodontia were classified into syndromic and non-syndromic according to the occurrence of tooth agenesis with or without systemic developmental defects. As for the advancement of theories and techniques of molecular genetics, a number of gene mutations have been identified to be the direct etiological factors causing some specified diseases, especially those with developmental defects. Here, this article summarized the outcomes of molecular genetic study of some cases we collected. Of the systemic oligondontia patients, a new four-base-deletion mutation in PITX2 was identified in a large kindred with typical symptoms of Rieger Syndrome; four different gene mutations in ED1 casing X-linked hypohidrotic ectodermal displasia were found in five nucleus families. Compared with the former, non-syndromic oligodontia has more genetic heterogeneity rather than some specific virulence gene. PAX9 and MSX1 are the identified genes associated with family tooth agenesis without systemic syndrome. Also, in our research, three gene mutations in CBFA1 were detected in four cleidocranial dysplasia families, which is a systemic developmental disease including the symptoms of tooth eruption abnormality and accessory teeth.