Vir- (avirulent) strains of B, pertussis were selected, via increased resistance to erythromycin, which were isogenic with parental Vir+ strains. Chromosomal DNA from these pairs of strains were studied with a number of probes and with methylation-sensitive restriction endonucleases. These experiments suggested that DNA rearrangements were not involved in the Vir+ to Vir switch, and that the methylation status of the DNA was not altered during the switch. A B, pertussis gene library was probed with an oligonucleotide specific for the fimbrial subunit genes. This probe revealed that the chromosome of B. pertussis strain Taberman contained three fimbrial subunit genes:- i) an active fim 3 gene, ii) an inactive fim 2 gene, and iii) a gene dissimilar from the previously characterised fim X gene. The behaviour of the fim 3 gene in various AGG 3-strains was investigated, and these studies revealed that a cis-acting factor was responsible for inactivation of the chromosomal fim 3 gene in these strains. It was also shown that the fim 3 locus encoded fimbrial structures when conjugated into an afimbrial B. pertussis strain. No evidence was found to suggest that DNA rearrangements were Involved in serotype variation. A probe made from the hin gene, which controls the invertible region of Salmonella typhimurium, was found to hybridise to chromosomal DNA from B, pertussis, under reduced stringency conditions. The gene library was probed with this probe and a cosmid clone Isolated, This clone did not appear to produce an active invertase in E. coli, when tested in two different inversion assays. An oligonucleotide probe was produced which was homologous with the recombination sites recognised by the hin-like family of invertase proteins and this also hybridised to B. pertussis chromosomal DNA under reduced stringency conditions