The histological parameters of Helicobacter pylori (H. pylori) gastritis are dependent on the virulence factor profile of the microbe, which includes the cytotoxins vacA (vacuolating cytotoxin A) and cagA (cytotoxin-associated gene A) as well as the duration of infection. The virulence factor genotypes vacA and cagA were assessed by the line probe reverse hybridization assay INNO-LiPA and correlated with the histological parameters of H. pylori infection, in particular intestinal metaplasia (IM) as well as with the patient's age. A total of 120 patients were analyzed; 47 patients with IM in the antrum and 73 control patients without this alteration. The vacA s1 cagA+ genotype (high virulence) correlated with the presence of antral IM, a more intense acute inflammation in both antrum and corpus and the formation of ulcer. The vacA m1 genotype (high virulence) correlated with a more intense acute inflammation in only the corpus as well as more prominent Russell bodies in the antrum. H. pylori strains with the vacA s2 m2 cagA- genotype (low virulence) were rarely found in these conditions (all P <0.05). No correlation with the virulence status was found for the type and extent of IM, the intensity of chronic inflammation, the formation of lymphoid follicles and the microbial density. Furthermore, patients with IM were 7 years older than their counterparts without (P<0.05). Finally, there was a trend for more virulent vacA s1 m1 cagA+ strains to be found in younger individuals (P>0.05). The virulence genotype of the microbe is an important determinant for the severity of the gastritis and the formation of antral IM. Age is an additional factor for the development of IM.