AIMS: To test whether a hypoacidic environment may potentially "stress" Helicobacter pylori DNA, encouraging the emergence of strain variation. METHODS: This hypothesis was tested by inducing prolonged hypoacidity with omeprazole, a potent antisecretory drug. The genomic DNA of H pylori was studied by electrophoretic separation of restriction endonuclease fragments followed by rRNA gene hybridisation in seven patients infected with H pylori before and after treatment with omeprazole 20-40 mg daily for six to eight weeks. DNA was isolated and purified using the guanidium thiocyanate reagent method. DNA samples were digested with Hae III, electrophoresed, vacublotted, and hybridised using a biotinylated cDNA probe prepared from 16S and 23S rRNA from H pylori NCTC 11638. Isolates were compared using their ribopatterns (DNA fingerprints). RESULTS: A total of 26 isolates were obtained; all DNA isolates were cut by Hae III, which was the enzyme that gave the best resolved hybridisation patterns for analysis. No two patients harboured the same strain. The isolates from two patients showed evidence of subtypic variation; one patient had two distinct strains and four patients had their own indistinguishable strains before and after treatment with omeprazole. For each patient, the paired ribopatterns of H pylori DNA were not affected by treatment with omeprazole for six to eight weeks. CONCLUSION: The H pylori genome is relatively stable when exposed to the conditions of prolonged hypoacidity that result from treatment with omeprazole.