Cleft lip and palate (CLP) is one of the most prevalent congenital craniofacial anomalies. It has a significantly greater incidence of dental abnormalities in number, size, shape, and eruption of the teeth. Knout-out mouse model can identify several genes which play an important role in tooth agenesis. Since disruption of these genes has been confirmed to result in tooth agenesis in humans, CLP associated with hypodontia may be the best models for isolated tooth agenesis. According to the studies of dental abnormalities in CLP, the severity of dental defect is known to be influenced by the CLP phenotype. The cumulative data obtained from mouse and human genetic studies indicated that MSX1, PAX9 and AXIN2 are considered as candidate genes in non-syndromic hypodontia, while Shh, Pitx2, Irf6, p63 and EDA pathway genes are involved in syndromic one. We expect that genetic approach of CLP can offer the basis for tooth regeneration and be a new target in hypodontia therapy.