In a search for methods for subtyping of Bartonella henselae in clinical samples, we amplified and sequenced a 701-bp region in the 3' end of the ftsZ gene in 15 B. henselae isolates derived from cats and humans in the United States and Europe. The ftsZ sequence variants that were discovered were designated variants Ph ftsZ 1, 2, and 3 and were compared with 16S rRNA genotypes I and II of the same isolates, There was no ftsZ gene variation in the strains of 16S rRNA type I? all of which were Bh ftsZ I. The type II strains constituted two groups, with nucleotide sequence variation in the ftsZ gene resulting in amino acid substitutions at three positions, one of which was shared by the two groups. One 16S rRNA type II isolate had an ftsZ gene sequence identical to those of the type I strains. Variants Bh ftsZ I and 2 were detected in tissue specimens from seven Swedish patients with diagnoses such as chronic multifocal osteomyelitis, cardiomyopathy, and lymphadenopathy, Patients with similar clinical entities displayed either Bh ftsZ variant, The etiological role of B. henselae in these patients was supported bg positive Bartonella antibody titers and/or amplification and sequencing of a part of the B, henselae gltA gene. B. henselae ftsZ gene sequence variation mag be useful in providing knowledge shout the epidemiology of various B. henselae strains in clinical samples, especially when isolation attempts have failed. This report also describes manifestations of atypical Bartonella infections in Sweden.