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Enrofloxacin and doxycycline are antimicrobial agents used to treat bacterial diseases of cats. In vitro susceptibility data indicate that either drug should be effective against Bartonella species. In vivo efficacies of these drugs for eradication of chronic Bartonella henselae or Bartonella clarridgeiae infections were examined in 18 experimentally infected cats and 25 naturally exposed cats treated with enrofloxacin (22.7 mg given orally [PO] every 12 h [q12h] [14 days, n = 10; 28 days, n = 13]) or with doxycycline (25 mg PO q12h [14 days, n = 9; 28 days, n = 8]) or not treated (n = 3). Plasma drug concentrations were determined in experimental cats by high-performance liquid chromatography. Only 23 of 43 cats enrolled ultimately met inclusion criteria. Bacteremia was eliminated for 12 to 25 weeks posttreatment in four of seven cats receiving 14 days of enrofloxacin, five of seven cats receiving 28 days of enrofloxacin, one of six cats receiving 14 days of doxycycline, and one of two cats receiving 28 days of doxycycline. Defining a negative result by blood culture as treatment success may be erroneous; these results may reflect the insensitivity of blood culture or the relapsing nature of Bartonella bacteremia. Our results suggest that MICs obtained with axenic media do not predict antimicrobial activity against intracellular Bartonella, that a long treatment course is required to eliminate infection, and that duration of therapy correlates with pretreatment bacterial load. Given current concern about the development of antimicrobial resistance, we would reserve recommendation for treatment to cats owned by an immunocompromised individual or as an alternative to euthanasia of a pet.