It is commonly believed in the Western World that the more severe forms of gastroduodenal diseases like peptic ulcer are associated with infection by specific Helicobacter pylori strains classified as type I being considered to be more virulent than type II strains. However, in Korea, most of H. pylori isolates belong to type 1 strains regardless of virulence. Type I H. pylori strains differ from type II strains by the presence of the cag pathogenicity island (cag PAI) composed of a block of genes. In this study, the nucleotide sequence of cag PAI of the H. pylori Korean strain 51 was determined and compared with those of strains 26695 and J99 to assess the structural variation in the region and to evaluate its implication in the virulence of the H. pylori. The cag PAI of H. pylori strain 51 was smaller in size and in the number of constituting ORFs in comparison with 26695 and J99 strains. Although many cag orthologues were nearly identical one another with the similarity of 90% or more at the nucleotide and amino acid levels, there were some remarkable and significant differences in several cag genes among the three cag PAIs. Surprisingly, the percent similarities at amino acid level were lower than those at nucleotide level in one third of the ORFs. The two genes (cag7 and cagA) of strain 51 differed in sizes and deduced amino acid sequences from the corresponding genes of the other two strains. When comparing cagA ORF of H. pylori strain 51 with that of 8 non-Korean strains, phylogenetic tree revealed that the strain 51 formed a separate branch with the most far distances from the other strains except for a Japanese strain. The Cag7 protein of, strain 51 had a deletion in the repeat region II, suggesting a major change in the conformation and function of the protein.