Data is presented on the identification and characterisation of 14 chromosomal integration loci of the insertion element IS901 on the Mycobacterium avium (cervine strain JD88/118) genome. Thirteen of these integration loci have been mapped to their corresponding positions on individual contigs of the Mycobacterium avium (strain 104) genome (TIGR unfinished genome-sequencing project). One further integration locus, which could not be correlated with strain 104 (an IS901- strain), was shown to consist of at least 2 copies of IS901 lying in tandem. Nucleotide sequence analysis of 5( and 3( flanking sequences revealed putative ORFs on both plus- and minus-strands that are interrupted as a direct consequence of IS901 integration. One of the plus-strand ORFs was positively identified as the catalase HPII (katE) gene although no recognisable -10 or -35 promoter sequences could be detected upstream of the initiation codon. Database searches using an additional 65 plus-strand ORFs and a further 74 minus-strand ORFs revealed no significant homology with any other known genes. A consensus IS901 insertion target sequence compiled from 11 integration sites was in broad agreement with earlier reports that were based on only 2 such loci.