PURPOSE: To explore the association between the risk of dental caries and distal-less homeobox 3 (DLX3) gene in Chinese children. MATERIALS AND METHODS: Based on the decayed, missing, and filled teeth (dmft) score, the children were divided into a control group (dmft = 0) and a case group (dmft ≥ 1). DLX3 gene (rs11656951 and rs2278163) polymorphisms were genotyped by polymerase chain reaction (PCR) and Sanger sequencing methods. Possible association of DLX3 gene (rs11656951 and rs2278163) polymorphisms with dental caries risk was assessed using the chi-squared test. Subgroup analysis of association was assessed by logistic regression analysis for the potential risk factors. RESULTS: The age at which toothbrushing was started, the brushing frequency, brushing with fluoride toothpaste, and regular dental visits were statistically significantly different between case and control groups (p 0.05). The frequencies of rs11656951 TT genotype and T allele were statistically significantly higher in the control group than in the case group. The chi-squared test showed that CT genotype (p = 0.026, OR = 0.613, 95%CI = 0.398-0.944) and TT genotype (p = 0.001, OR = 0.378, 95%CI = 0.212-0.673) were negatively correlated with caries susceptibility. The T allele of rs11656951 was more frequently discovered in the control group, and was statistically significantly associated with decreased caries susceptibility (p = 0.001, OR = 0.636, 95%CI = 0.486-0.831). The G allele of rs2278163 was obviously correlated with elevated caries susceptibility (p = 0.049, OR = 1.314, 95%CI = 1.000-1.725). DLX3 gene rs11656951 TT genotype was a protective factor for caries susceptibility in the subgroups gender, sweets intake, eating before sleep, brushing frequency, brushing with fluoride toothpaste, and dental visits. The GG genotype of rs2278163 was a risk factor for caries in subgroups eating before sleep, brushing without fluoride toothpaste, and regular dental. The TT genotype of rs11656951 was dramatically correlated with reduced caries risk in low (p = 0.004, OR = 0.387, 95%CI = 0.202-0.742) and moderate/high (p = 0.016, OR = 0.360, 95%CI = 0.154-0.840) groups. CONCLUSION: DLX3 gene rs11656951 TT genotype is a protective factor and rs2278163 GG genotype is a risk factor for caries susceptibility, especially in low and moderate/high subgroups.