Municipal water, treated waste-water and well-water from all 25 counties in Sweden were analysed for the presence of Helicobacter spp. DNA. Bacteria were concentration by immunomagnetic separation. Culture, Gram staining and urease tests were performed before lysis of bacteria. Two polymerase chain reaction (PCR) assay with high sensitivity (adhesin and 16S rRNA) were followed by Helicobacter spp. specific hybridization. Nine of 24 private wells, three of 25 municipal tapwater and three of 25 wastewater samples were positive for both PCR assays. Positive municipal and waste-water samples were positive for counties. Non-specificity of PCR methods due to the presence of unknown bacteria within the genus helicobacter cannot be totally ruled out. Thus, the clinical significance of findings Helicobater spp. DNA in drinking water needs to be further evaluated.