Congenital agenesis of permanent and/or primary teeth is one of the most common orofacial developmental disorders. Although environmental factors can also affect tooth agenesis, genetic factors play a more important role. It can be classified into nonsyndromic and syndromic hypodontia. MSX1, PAX9, DLX1, DLX2, Activin beta-A, Activin receptor types IIA and IIB, and SMAD2 have been considered related to the former. Syndromic congenitally missing teeth is related to ectodermal dysplasias, Van der Woude syndrome and other syndromes. In this article, we will review the molecular genetic mechanisms of congenitally missing teeth. Keywords: congenitally missing teeth, hypodontia, mechanisms, molecular genetics