Helicobacter pylori is a Gram‐negative bacterium that infects the human gastric mucosa, causes gastritis and contributes to the development of peptic ulcers and gastric cancer. To facilitate molecular genetic analysis of this pathogen, we constructed a ∼20‐fold redundant cosmid library and physical/genetic map of strain NCTC11638. Genomic DNA fragments were cloned into the cosmid vector Lorist6, and clones were ordered by hybridization with several types of probes: (i) ends of cloned DNAs; (ii) chromosomal Notl digest fragments; (iii) cosmids containing Notl sites; and (iv) specific genes. Seven hundred and fifty‐one cosmids were mapped to one of thrM contigs covering > 90% of the chromosome, and are represented by a 68‐cosmid miniset. The order of cosmids was confirmed and extents of overlap among them were estimated by restriction analysis.

All currently known H. pylori genes were mapped, including those for a cytotoxin (vacA), cytotoxin‐associated protein (cagA), urease and regulatory functions (ureAB, ureD and ureH), catalase (katA), major and minor flagellins (flaA and flaB), heat‐shock (stress) and chaperone proteins (dnaK, htrA, hspB (groE_L)), prokaryotic ferritin (pfr), an adhesin subunit (hpaA), a surface protein (26kDa), and 16S and 23S ribosomal RNAs (two genes each). The orientations of eight genes or clusters were determined, and two repetitive sequences were also found. The gene order and rRNA gene copy number determined here differed from that reported for an unrelated strain, which suggests considerable flexibility in H. pylori genome organization.