A 16S ribosomal DNA-based PCR appeared to be a sensitive test for the detection of infection by Helicobacter pylori in 31 patients when compared with culturing and histological and serological techniques. For five patients, PCR was the only test with a positive result. H. pylori DNA was also found in gastrointestinal equipment even after standard intensive combined manual and machine cleaning. We therefore conclude that a reliable validation of PCR for the detection of H. pylori in gastric biopsy specimens is possible only when the cleaning and disinfection method used has been proven to remove all H. pylori DNA from gastrointestinal equipment. An adequate cleaning and disinfection method for the removal of H. pylori DNA from fiberoptic endoscopes is described.