Molecular genetics are difficult to perform in Bartonella henselae, the causative agent of cat scratch disease and the vasculoproliferative disorders bacillary angiomatosis and bacillary peliosis. To elucidate the underlying bacterial pathogenic mechanisms, genetic manipulation of B. henselae is the method of choice. We describe how to perform transposon mutagenesis in B. henselae using transposome technology. B. henselae mutants revealed by this technique showed random transpositional insertion into the chromosome. In contrast to transposon mutagenesis by conjugational transfer, transposome technology allows transposon mutagenesis of early passaged Bartonella spp. with approximately 100-fold higher efficiency. The results show that transposome technique is a rapid, efficient and simple method to generate transposon mutants of B. henselae.