The BvgAS signal transduction system in Bordetella spp. mediates a transition between infectious (Bvg+) and non-infectious (Bvg-) phases by sensing environmental conditions and regulating gene expression. Using differential display, arbitrary-primed polymerase chain reaction (PCR), we identified a gene expressed in the Bvg+ phase of Bordetella bronchiseptica that shows a high degree of sequence similarity to a locus involved in providing energy for type III secretion in pathogenic gram-negative bacteria (yscN in Yersinia spp.). We determined that the expression of this homologue in B. bronchiseptica (designated bscN) is regulated by bvg. Several open reading frames surrounding the bscN locus also show sequence similarity to loci encoding type III secretion apparatus components in other bacteria. An in-frame deletion of bscN in B. bronchiseptica leads to decreased secretion of several proteins, decreased cytotoxicity towards cultured cell lines and a defect in causing tyrosine dephosphorylation of specific proteins in infected cells in vitro. The deletion strain also revealed that bscN-mediated secretion is required for persistent colonization of the trachea in a rat infection model. Loci encoding type III secretion homologues were identified in four strains of B. pertussis and two strains of B. parapertussis. B. pertussis strain 18323 and an ovine isolate of B. parapertussis show significant transcription of the genes in vitro.