Approximately 50% of Helicobacter pylori isolates produce a cytotoxin in vitro that induces vacuolation of eukaryotic cells. Screening a lambda ZapII library of H. pylori 60190 chromosomal fragments permitted the identification of a 3864-base pair (bp) open reading frame (vacA) that encoded the vacuolating cytotoxin, and a > or = 567-bp upstream gene that was homologous to Escherichia coli cysteinyl-tRNA synthetase. The sequence data suggest that a 33-amino-acid leader sequence and a C-terminal peptide are cleaved from a 139-kDa protoxin to yield the mature 87-kDa cytotoxin. The vacA gene product contains a C-terminal motif that is present in several other bacterial proteins that undergo C-terminal cleavage, including IgA proteases of Haemophilus influenzae and Neisseria gonorrhoeae. Isogenic H. pylori mutants with insertional mutation of the vacA gene lacked vacuolating cytotoxin activity and failed to produce the 87-kDa protein. Southern analysis of naturally occurring tox-H. pylori strains with vacA probes indicated the presence of hybridizing bands, but both Southern analysis and polymerase chain reaction studies suggested that the vacA sequences of tox- strains differed from those of tox+ strains. Sequence analysis of a 1541-bp region of polymerase chain reaction-amplified vacA from tox- strain 87-203 indicated 64.8% amino acid identity with the corresponding region from tox+ strain 60190. Thus, sequence divergence in vacA genes may explain the lack of functionally active cytotoxin production by some H. pylori isolates.