The fimbriae of Bordetella pertussis are required for colonisation of the human respiratory tract. Two serologically distinct fimbrial subunits, Fim2 and Fim3, having been considered important vaccine components for many years, are included in the Sanofi Pasteur 5-component acellular pertussis vaccine, and the World Health Organisation recommends the inclusion of strains expressing both fimbrial serotypes in whole cell pertussis vaccines. Each of the fimbrial major subunit genes, fim2, fim3, and also fimX, has a promoter poly(C) tract upstream of its -10 box. Such monotonic DNA elements are susceptible to changes in length via slipped-strand mispairing in vitro and in vivo, which can potentially cause on/off switching of genes at every cell division. Here we describe intra-culture variability in poly(C) tract lengths and in the resulting fimbrial phenotypes in 22 recent United Kingdom B. pertussis isolates. Owing to the highly plastic nature of the fimbrial promoters, we used the same cultures for both genome sequencing and flow cytometry. Individual cultures of B. pertussis each contained multiple fimbrial serotypes and multiple different fimbrial promoter poly(C) tract lengths, which supports earlier serological evidence that B. pertussis expresses both serotypes during infection.