Objective. To investigate the association between the rs13347 polymorphism of the CD44 gene and the risk of kidney stone disease (KSD) in the Han population of northeast Sichuan, China, so as to provide a theoretical basis for the treatment of KSD. Methods. We used PCR-restriction fragment length polymorphism (RFLP) technique to perform genotyping at rs13347 locus of the CD44 gene in the KSD group and the gontrol group. SNP Hardy-Weinberg equilibrium (HWE) testing was used to confirm the balance of genetic inheritance. Multivariate logistic regression analysis was used for the assessment of rs13347 polymorphism and the risk of developing KSD and to compare the relationship between the polymorphism of rs13347 and clinical characteristics of patients with KSD. Results. Genotypic results of rs13347 locus of the CD44 gene in the two groups were consistent with the SNP-HWE test, indicating the genetic balance. At the same time, multivariate logistic regression analysis indicated that subjects with CT and TT genotypes at rs13347 in the CD44 gene were more likely to have KSD, and there was a higher prevalence rate in males. Furthermore, carrying allele T at rs13347 was also a risk factor for KSD. In addition, people carrying CT and TT genotypes at rs13347 also have a significantly increased risk of relapsing KSD. Conclusion. The rs13347 polymorphism of the CD44 gene may be associated with the risk of KSD in the Han population of northeast Sichuan in China, and the recurrence rate of KSD in the carriers of CT and TT genotypes is higher.