The influence of the proton pump inhibitor lansoprazole on strain diversity in Helicobacter pylori infected patients was investigated. Multiple isolates of Helicobacter pylori obtained pre-and post-therapy from gastric antral and body biopsies in 22 patients were compared using the random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) for analysis. Post-therapy strains exhibiting novel RAPD-profiles were found in 5 of 22 patients (4 of 11 patients treated with lansoprazole alone and 1 of 11 patients treated with lansoprazole plus amoxicillin), Proton pump inhibition may affect the microecology of the stomach by influencing the colonisation patterns of specific strains.