This is a descriptive study designed to correlate diagnostic real-time PCR results with histopathologic lesions in cats with clinical signs of upper respiratory infection (URI).The study occurred over a 9-month period in a single open-intake animal shelter. Cats that were selected for euthanasia by the shelter staff and additionally had URI were included in the study, for a total of 22 study cats. Combined conjunctival and oropharyngeal swab specimens were tested by quantitative real-time PCR (qPCR) for feline herpesvirus type 1 (FHV-1), feline calicivirus (FCV), Mycoplasma felis, Chlamydophila felis, and Bordetella bronchiseptica. Necropsy was performed on all cats, and a complete set of respiratory tract tissues was examined by histopathology. Among 22 cats, 20 were qPCR positive for FHV-1, 7 for M. felis, 5 for FCV, 1 for C. felis, and 0 for B. bronchiseptica. Nine cats were positive for two or more pathogens. Histopathologic lesions were present in all cats, with consistent lesions in the nasal cavity, including acute necroulcerative rhinitis in 16 cats. Histologic or antigenic detection of FHV-1 was seen in 18 of 20 cats positive for FHV-1 by qPCR. No lesions that could be specifically attributed to FCV, M. felis, or C. felis were seen, although interpretation in this cohort could be confounded by coinfection with FHV-1. A significant agreement was found between the amount of FHV-1 DNA determined by qPCR and the presence of specific histopathologic lesions for FHV-1 but not for the other respiratory pathogens.Upper respiratory infection (URI) is the most frequent disease reported in the 2 million to 6 million cats estimated to pass through United States shelters each year. Feline URI results from a complex, multifactorial interaction of respiratory pathogens, stress, and animal susceptibility. Intensive housing of cats, such as that found in animal shelters, catteries, and multicat households, can contribute to disease both by compromise to the host (stress, travel, poor health status) and by exposure, dose, and, potentially, evolution of the contributing pathogens. Although mortality is low, clinical signs of URI are discerning criteria in many shelters for euthanasia, so the consequences for affected cats are profound. Moreover, chronic, recurrent rhinosinusitis, considered incurable, may be a sequela of acute rhinitis (10).Many epidemiologic and diagnostic studies have identified five pathogens commonly associated with feline URI, which are feline herpesvirus type 1 (FHV-1), feline calicivirus (FCV), Bordetella bronchiseptica, Mycoplasma felis, and Chlamydophila felis (1,5,9,15,17,21). Clinical and diagnostic investigation is complicated for a number of reasons: clinical signs of infection with any one or combination of these five pathogens are overlapping and often nonspecific. Vaccination, common for FHV-1, FCV, and C. felis, can attenuate but is not protective of disease and/or shedding (14,16,20), and lastly, all of these microbes can be carried by and detected in clinically normal cats either as lat...