Although the role of fimbriae in bacterial disease has been well established, little is known about the function of Bordetella pertussis fimbriae. To study this function, well-defined fimbrial mutants were constructed. B. pertussis harbours three fimbrial genes, fim2, fim3 and fimX, and strains were constructed in which one or more fimbrial genes were inactivated by means of gene replacement. Analysis of these strains by means of immunoblotting suggested the presence of a fourth fimbrial gene, tentatively designated fimY. A fimbrial mutant was analysed in a mouse respiratory infection model, together with a strain harbouring a deletion in the gene for the filamentous haemagglutinin. Both mutants were affected in their ability to persist in the trachea. Persistence in the nasopharynx was only affected by the mutation in the filamentous haemagglutinin gene. Neither the filamentous haemagglutinin nor the fimbrial mutants were affected in their ability to persist in the lung. Our results suggest that the filamentous haemagglutinin plays a more crucial role than fimbriae in the colonization of the upper respiratory tract of the mouse.