Stomach Cancer is third most prevalent cancer worldwide and most common gastrointestinal cancer in Iran.Several studies showed relationship between Helicobacter pylori and Stomach Cancer. Some studies in countries with low socioeconomic status and poor water supply indicated the importance of environmental factors specially water sources.Since prevalence rate of H.pylori infection in Khuzestan province was about 57%,we decided to investigate about presence of the bacteria in raw and drinking water of Ahvaz city using Polymerase Chain Reaction (PCR) method. Also physicochemical characteristics of water samples examined to determine role of them on presence or absence of Helicobacter pylori. Water samples were collected from River and water taps in consumption points. Obtained water sample examined by PCR method. PCR examination for all 45 water samples was negative, and we could not detect H.pylori bacteria in water samples. In River water samples, high turbidity and presence of several organic, inorganic materials, also low concentration of H.pylori DNA and transform spiral form of H. pylori to coccoid form and In treated water samples, high residual chlorine and pH can destroy H.pylori DNA, low concentration of H.pylori DNA and low sensitivity of PCR method for detection of H.pylori in water samples made detection it difficult by PCR.