OBJECTIVE To assess the degree of restriction fragment length polymorphism (RFLP) in the Helicobacter pylori adhesin gene hpaA and to determine the molecular basis of RFLP in this gene. METHODS A 375-bp, polymerase chain reaction-amplified internal sequence of hpaA, obtained from 50 different H. pylori isolates, was restricted with Sau3A and HinfI, individually. Polymerase chain reaction products representing different RFLP types were sequenced. RESULTS Seven different polymorphic types were found in hpaA. Base substitutions at only four positions, two in Sau3A and two in HinfI sites, account for all of the RFLP types, including the size of the restriction fragments determined by gel electrophoresis. Most, 90%, of the base substitutions are very conservative, i.e., either do not change the encoded amino acid or substitute a homologous amino acid, and cause no detectable antigenic or functional effect on hpaA. The region of hpaA encoding the receptor-binding motif was particularly well conserved. CONCLUSIONS RFLP typing of hpaA using Sau3A and HinfI provides an additional tool for comparing the genetic relatedness of H. pylori isolates collected during epidemiological and/or treatment studies.