Selective tooth agenesis is a congenital disorder divided into two types based on the number of missing teeth, i.e. hypodontia which is the absence of <6 teeth and oligodontia which is agenesis of >6 permanent teeth excluding the third molars. As the prevalence of tooth agenesis is higher in populations with Arab and Asian descent, it is intriguing to probe deeper into the molecular aspects of this disorder. Selective tooth agenesis inherits as autosomal dominant, autosomal recessive or X-linked dominant mode of inheritance. The 10 loci identified are selective tooth agenesis 1 through 9 and selective tooth agenesis X1. Genes for 8 of these loci have been characterised while the causative genes for selective tooth agenesis 2 and 5 still remain to be elucidated. The current broad-spectrum review was planned to discuss the molecular genetics of all 10 loci mapped with selective tooth agenesis, their mode of inheritance as well as the proteins encoded by these genes, their roles and their interactions.