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Background  Many bacteria and archaea possess a defense system called clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (CRISPR-Cas system) against invaders such as phages or plasmids. This system has not been demonstrated in  Helicobacter pylori . The numbers of spacer in CRISPR array differ among bacterial strains and can be used as a genetic marker for bacterial typing.    Results  A total of 36  H. pylori  isolates were collected from patients in three hospitals located in the central (PBH) and southern (SKH) regions of Thailand. It is of interest that CRISPR-like sequences of this bacterium were detected in  vlpC  encoded for VacA-like protein C. Virulence genes were investigated and the most pathogenic genotype ( cagA vacA  s1m1) was detected in 17 out of 29 (58.6%) isolates from PBH and 5 out of 7 (71.4%) from SKH.  vapD  gene was identified in each one isolate from PBH and SKH. CRISPR-like sequences and virulence genes of 20 isolates of  H. pylori  obtained in this study were analyzed and CRISPR-virulence typing was constructed and compared to profiles obtained by the random amplification of polymorphic DNA (RAPD) technique. The discriminatory power (DI) of CRISPR-virulence typing was not different from RAPD typing.    Conclusion  CRISPR-virulence typing in  H. pylori  is easy and reliable for epidemiology and can be used for inter-laboratory interpretation.    Electronic supplementary material  The online version of this article (10.1186/s13099-017-0215-8) contains supplementary material, which is available to authorized users.

CRISPR-like sequences in Helicobacter pylori and application in genotyping