[Objective] To detect the distribution of CRISPR/Cas system in Shigella clinical strains and to analyze the relationship between CRISPR/Cas system and virulence genes. [Methods] We used 10 pairs of primers of PCR assay for detection of the CRISPR/Cas system including CRISPR1, cas2-cas1 genes, cas6e-cas5 genes, cas7 gene, cse2 gene, cse1-cas3 genes and virulence genes including ipaH, ial, ipaBCD, virA in 57 Shigella strains. The CRISPR sequences were analyzed using CRISPR finder. The relativity between the presence of CRISPR/Cas system and virulence gene was analyzed by χ2 -test. [Results] Among the 57 strains of Shigella, the number of spacers is little and its sequences have similarity among different strains. The positive rate of CRISPR/Cas system is 84.2%. However, 68.8% of Shigella strains analyzed contained insertion sequencese in cse2 gene or cas6e-cas5 gene. The positive rates of ipaH, ial, virA and ipaBCD is 100%, 100%, 98.2% and 87.7%, respectively. No statistical difference was found between the distribution of active-CRISPR/Cas system and the ipaBCD gene. [Conclusion] CRISPR/Cas system was widely distributed in Shigella clinical strains. Insertion sequences were presented in some strains. Our analysis of CRISPR/Cas system did not reveal a potential link between its presence and the virulence genes in Shigella clinical isolates.