AIMS--To see whether the activity of omeprazole on Helicobacter pylori is associated with toxicity of strains; to determine whether omeprazole inhibited vacuolisation of cells in culture induced by H pylori cytotoxin and by ureas, and if omeprazole prevented H pylori motility. METHODS--Minimal inhibitory concentrations (MICs) of omeprazole were determined for seven cytotoxic and five non-cytotoxic H pylori strains. Omeprazole at different concentrations was incubated with cytotoxic and non-cytotoxic extracts of H pylori, or with purified H pylori urease, and added to cells in culture. Inhibition of motility by omeprazole was tested in semi-solid medium. RESULTS--MIC90 of omeprazole was 40 micrograms/ml. MICs for cytotoxic and noncytotoxic organisms were similar. Omeprazole did not prevent vacuolisation induced by the cytotoxic extract, but at high concentrations it inhibited the formation of vacuoles induced by urease. Motility was not inhibited by the drug. CONCLUSIONS--H pylori cytotoxin is not the target of the antimicrobial activity of omeprazole. Should the drug reach clinically effective concentrations in vivo, it could potentially prevent the mucosal damage caused by the vacuolising activity of urease.