Populations of Helicobacter pylori cells show a stable expression of Lewis surface antigens, although phase variation may occur among individual organisms grown in vitro. We searched for variation in Lewis phenotypes among H. pylori cells of minimally in vitro-passaged isolates. Lewis expression in 180 clonal H. pylori populations from the primary culture of 20 gastric biopsy samples from 12 patients, and that in 160 isolates from primary cultures from 16 experimentally infected rodents, were examined by enzyme immunoassays. Substantial differences in Lewis expression were found among the isolates from 9 (75%) of 12 patients. These differences were unrelated to overall genetic diversity as determined by polymerase chain reactions for random amplified polymorphic DNA or cagA status, and they persisted during subsequent in vitro passage. In contrast, Lewis expression was highly uniform in H. pylori isolates from different rodents infected for up to 20 weeks. Variation in H. pylori Lewis expression in genetically closely related organisms in human subjects may provide a pool of bacterial phenotypes for the continuous selection of optimally host-adapted populations suitable for persistence.