In conclusion, no significant associations between SNPs in DDX39B and MPO genes and dental caries were found in the present study; however, a tendency could be observed, as well as between initial caries and polymorphisms in VDR, LTA, and MMP3. SNPs in other genes were also investigated, but none of these showed a significant relationship, not either for initial caries. Here, DDX39B is linked to dental caries.