Background: Upper respiratory tract disease (URTD) of cats is caused by a number of pathogens, including Chlamydophila felis and Mycoplasma spp. For effective treatment of both infections, doxycycline and enrofloxacin are recommended, but adverse effects limit their use in cats.Hypothesis: That the fluoroquinolone pradofloxacin is effective against C. felis and Mycoplasma infection in cats with URTD or conjunctivitis.Animals: Thirty-nine cats with signs of URTD or conjunctivitis. Methods: Placebo-controlled, double-blind clinical trial. Cats were randomly entered into 1 of 2 treatment groups: treated PO with either 5 mg/kg pradofloxacin q24h or 5 mg/kg doxycycline q12h for 42 consecutive days. Changes in health status and clinical scores were evaluated. The presence of C. felis and Mycoplasma spp. was determined by quantitative polymerase chain reaction (PCR) and nested PCR of conjunctival swabs, respectively.Results: At the beginning of the study, C. felis and Mycoplasma spp. were detected in 23 and 20 cats, respectively. Cats of both groups responded rapidly with a marked improvement in clinical signs within the 1st week. During treatment with either drug, C. felis DNA copy number declined quickly. Complete elimination of Mycoplasma spp. was achieved in both groups; however, whereas all cats receiving doxycycline eliminated C. felis, 4 cats treated with pradofloxacin remained PCR-positive.Conclusion and Clinical Importance: This study demonstrates that both pradofloxacin and doxycycline have good efficacy against C. felis and Mycoplasma spp., resulting in a marked improvement of clinical signs. However, C. felis DNA remained in some cats after treatment with pradofloxacin, suggesting that infection might not have been eliminated.