A novel nonhemolytic phase variant of Bordetella pertussis was characterized. This strain is strongly impaired in the transcription of the pertussis and adenylate cyclase toxins, whereas other known virulence-related factors such as the filamentous hemagglutinin, the fimbriae, and the outer membrane protein pertactin are expressed and regulated normally. Complementation and allelic exchange experiments demonstrated that the mutation is localized neither in the bvg locus involved in virulence regulation nor in the genes responsible for synthesis and transport of the toxins pertussis and adenylate cyclase. Instead, the mutation impairing transcription of at least the two toxin genes is located in a new genetic locus, which acts together with the BvgA/S two-component regulatory system on the expression of a subset of virulence genes. Further analysis suggested that most presumably the mutation affects a sequence-specific DNA-binding protein which contributes to transcriptional activation. The mutant was nonlethal in a murine respiratory model, which corresponds well with the lack of expression of the toxins. However, the clearing rate of this mutant from the lungs of mice was much lower than that of a bvg mutant, suggesting that factors other than the toxins may play a role in the persistence of the bacteria in the respiratory tract of mice.