The expression of virulence factors in the bacterium Bordetella pertussis is regulated in an environmentally responsive fashion under the control of the two-component system encoded by the bvgAS locus. In recent years we have focused research efforts on understanding the mechanisms of gene regulation in this important human pathogen - specifically focussing on the genes encoding pertussis toxin (ptx) and filamentous hemagglutinin (fha). Within the past year we have continued to analyze in detail the structure of the fha promoter and have defined critical regions and nucleotides involved in interaction with BvgA. Detailed sequence requirements for binding of BvgA to the P-fha binding site have been elucididated by a combination of biochemical and genetic methods. Similar examination of deletions within the promoter have demonstrated that two turns of the DNA helix (but not one or three turns) can be removed and still result in a promoter which is activated by BvgA, but which now has a higher level of expression in vivo. Together these results have increased our understanding of the mechanisms of virulence gene activation in this important human pathogen, and have continued to suggest ways that production of vaccine antigens may be increased. Other studies in the laboratory have addressed the genomic structure of natural isolates of B. pertussis from a recent outbreak. We found that gene order in the chromosomes of these strains was variable.