Tooth agenesis is the failure of tooth bud development, causing definitive absence of the tooth. It is the most common dental anomaly, affecting up to one-quarter of the general population. The main cause is related to abnormal function of specific genes which play key roles during odontogenesis, particularly MSX1 and PAX9. MSX1 is a transcription factor highly expressed in the mesenchyme of developing tooth germs, whereas PAX9 is a transcription factor that shows a direct relationship with craniofacial development, particularly the formation of the palate and teeth. Despite the high frequency of tooth agenesis, there are as yet only a restricted number of mutations in MSX1 and PAX9 that have been associated with non-syndromic tooth agenesis. Thus, a deeper analysis of the gene networks underlying this anomaly is imperative. By means of a literature review based on Medline, PubMed, Lilacs, NCBI, and STRING, performed between 1991 and 2010 and focused on etiologically associated mutations, this work aimed to assess the latest advances in the genetic etiology of tooth agenesis and to offer an insight into how they can assist dental practice in the near future. A better knowledge of the genetic networks underlying tooth agenesis will lead to better treatment options and, perhaps, a tool for early diagnosis possibly related to DNA examination based on polymorphic variants. Such a test based on DNA analysis may be available to and accessible by clinicians, resulting in a more accurate diagnosis and allowing for a better approach to this anomaly.