To study the relationships between single nucleotide polymorphisms (SNP) of gene msh homebox-1 (MSX-1) (rs3821949, rs12532) and sporadic tooth agenesis by filtering the susceptibility genes in a Jiangsu province population.DNA samples were extracted from 198 patients with sporadic tooth agenesis and 207 control subjects. Two MSX-1 gene polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The association between the genetic polymorphism and risk of sporadic tooth agenesis was estimated by chi(2) and logistic regression. The Phase was used to determine the Hardy-Weinberg equilibrium and haplotype association.In the population, the allele frequency and genotype rates of the SNP rs3821949 were significant different between the patients with sporadic tooth agenesis and normal controls: the A allele frequency in the patients (43.2%) was significantly higher than that in the normal controls (31.4%, P = 0.008), and the AA genotype rate of the patients (14.7%) was significantly higher than that of the controls (12.6%, P = 0.030). However, There were no significant differences in the allele frequency and genotype rates of the SNP rs12532 between the patients with sporadic tooth agenesis and normal controls. Similar results were obtained between the mandibular incisor agenesis cases and controls. The haplotype frequencies of GA (27.9%) were significantly lower in non-mandibular incisor agenesis cases group than that in the control group (37.0%, P = 0.03, OR = 0.51).The results show that SNP rs3821949, which is located at 5';near region of the MSX-1 gene, is likely to have an influence on the transcriptional activity of this gene and be associated with sporadic tooth agenesis. The haplotypes constructed with these 2 SNP sites may be linked with the susceptibility gene of non-mandibular incisor agenesis.