ABSTRACT. Tooth agenesis is one of the most common anomalies of human dentition. Recent genetic studies have provided information regarding a number of genes related to both syndromic and nonsyndromic forms of hypodontia. In a previous study, we found that polymorphism in rs11001553 of DKK1 was associated with hypodontia in the Chinese Han population. In this study, we extended this investigation to 89 individuals diagnosed with sporadic non-syndromic oligodontia (40 males and 49 females). These individuals were analyzed with 268 subjects (123 males and 145 females) diagnosed with nonsyndromic hypodontia and 190 healthy control subjects (99 males and 91 females). DNA was obtained from whole blood or saliva samples and genotyping was performed by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Significant differences were observed in the allele and genotype frequencies of rs11001553 of DKK1. These data demonstrated an association between rs11001553 of DKK1, a tooth development-associated gene, and non-syndromic tooth agenesis in Chinese Han individuals. This information may provide further understanding of the molecular mechanisms of tooth agenesis. Furthermore, DKK1 can be regarded as a marker gene for the risk of tooth agenesis.