The efficacy of DNA vaccines encoding filamentous hemagglutinin (FHA) and pertactin (PRN) antigens of Bordetella pertussis were evaluated using a murine respiratory challenge model. Mice immunised with a PRN DNA vaccine via the intramuscular route generated both humoral as well as cell-mediated immune responses, with strong systemic IgG titres and relatively moderate levels of IFN-γ in recombinant antigen-stimulated splenocyte supernatants. On the other hand, mice immunised with the FHA DNA vaccine by the same route, elicited a strong cell-mediated immune response as indicated by production of high IFN-γ levels detectable in the recombinant antigen-stimulated splenocyte supernatants. However, surprisingly mice immunised with the self-ligated pcDNA3.1 vector generated antibodies that were highly cross-reactive with recombinant FHA. After accounting for the cross-reactivity, no antibody response was attributable to the FHA-DNA vaccine. Following a sub-lethal aerosol challenge, partial clearance of the challenge infection was observed following immunisation with the FHA and PRN DNA vaccines with no clearance observed in the control groups including the vector-immunised mice. Given the incomplete clearance reported previously for our genetically detoxified S1 pertussis DNA vaccine it was apparent that an effective pcDNA3.1-based DNA vaccine against whooping cough may need to be administered as a cocktail vaccine encoding genetically inactivated pertussis toxin, FHA and PRN, preferably with boosting of the immune response with the recombinant proteins, to ensure effective long-lasting protection against whooping cough.