Tooth agenesis are the most common craniofacial malformations. Its prevalence in permanent dentition reaches 20% and its expressivity ranges from only one tooth, usually a third molar, to the whole dentition. Genetic linkage and molecular biology studies have allowed, in the last decade, the identification of mutations responsible for some patterns of syndromic and nonsyndromic tooth agenesis. The mutated genes are key genes for the development of dentition, like the ones that encode the transcription factors MSX1, PAX9 and PITX2, the signalling protein EDA and its receptor EDAR. Current research would lead to the development of new classifications of tooth agenesis that took into account both the phenotypes and the genetic background. This would allow an early diagnosis of the condition, before the development of the somatic defect, that could eventually be repaired with gene therapy or tissue and organ engineering.