AIM: Cytotoxin-associated protein (antigen) A (CagA)plays an important role in Helicobacter pylori(H pylori)pathogenesis. Our aim was to obtain cagA mutant strains by a new mutation method so as to better understand the mechanism of CagA in epithelial cells. METHODS: In contrast with the traditional method using suicide plasmid, we constructed cagA- mutant strains directly with PCR products. The constructed mutant clones grew on selective media and allelic exchange was confirmed by South blot. Furthermore, two different transformation methods, electroporation, and natural transformation, were compared with regard to the efficiency of recombination.RESULTS: The mutation by PCR products could be completed within 3-5 d, and the recombination rate by electroporation and natural transformation was 4.02×10-8 and 1.03x 10-9 respectively. Mutation rate by electroporation (4.02× 10-8) was far higher than by natural transformation (1.03× 10-9) (P = 0.000＜0.005).CONCLUSION: cagA- mutant strains have been constructed,which is important for further study on the function of CagA in epithelial cells. A mutation method by directly using PCR products has been proved successful with a much higher mutation rate, and is easier, especially when in combination with electroporation. This method could be widely used in gene deletion of H pylori.