AIM:To evaluate the in vitro effect of amoxicillin and clarithromycin on the cag pathogenicity island (cag PAI). METHODS:One hundred and forty-nine clinical isolates of Helicobacter pylori (H.pylori ) cultured from gastric biopsies from 206 Colombian patients with dyspeptic symptoms from a high-risk area for gastric cancer were included as study material.Antimicrobial susceptibility was determined by the agar dilution method.Resistant isolates at baseline and in amoxicillin and clarithromycin serial dilutions were subjected to genotyping (cagA , vacA alleles s and m ), Glu-Pro-Ile-Tyr-Ala (EPIYA) polymerase chain reaction and random amplified polymorphic DNA (RAPD).Images of the RAPD amplicons were analyzed by Gel-Pro Analyzer 4.5 program.Cluster analyses was done using SPSS 15.0 statistical package, where each of the fingerprint bands were denoted as variables.Dendrograms were designed by following Ward's clustering method and the estimation of distances between each pair of H. pylori isolates was calculated with the squared Euclidean distance. RESULTS:Resistance rates were 4% for amoxicillin and 2.7% for clarithromycin with 2% double resistances.Genotyping evidenced a high prevalence of the