Within the alpha subdivision of proteobacteria, the arthropod-borne human pathogens Rickettsia prowazekii and Bartonella henselae provide examples of bacteria with obligate and facultative intracellular life styles, respectively. The complete genome sequence of R. prowazekii has been published, whereas the sequencing of the B. henselae genome is in its final stage. Here, we provide a brief overview of a comparative analysis of both genomes based on the delineated metabolic properties. The relative proportion of genes devoted to basic information processes is similar in the two genomes. In contrast, a full set of genes encoding proteins involved in the biosynthesis of amino acids and nucleotides is present in B. henselae, while the majority of these genes is absent from R. prowazekii. This suggests that B. henselae has a better potential for growth in the free-living mode, whereas R. prowazekii is more specialised to growth in an intracellular environment. Functional genomics will provide the potential to further resolve the genetic basis for successful human infections by these important parasites.