ObjectivesThe objectives of this study were to determine the prevalence of canine infectious respiratory disease pathogens among asymptomatic client‐owned dogs, and to compare the risks of asymptomatic pathogen carriage between client‐owned dogs and dogs in an animal shelter.Materials and MethodsPooled tonsillar, conjunctival and nasal cavity swabs from asymptomatic client‐owned dogs (n=133) were tested using a real‐time polymerase chain reaction canine respiratory panel. Identical samples from asymptomatic dogs in an animal shelter (n=295) were similarly tested for selected pathogens. Risk differences were calculated between client‐owned dogs and shelter dogs for each of the respiratory pathogens included in the analyses.ResultsA total of 15 of 133 (11.3%) asymptomatic client‐owned dogs were positive for at least one pathogen in the complex. Seven dogs (6.1%) were positive for M. cynos, six (5.2%) were positive for B. bronchiseptica, two (1.7%) were positive for canine herpesvirus type 1 and two (1.7%) were positive for canine respiratory coronavirus. For all eight pathogens tested in both groups, the proportion of positive cases was higher among shelter dogs than among client‐owned dogs. Shelter dogs had a higher risk for M. cynos (0.18, 95% confidence interval: 0.12 to 0.25), canine respiratory coronavirus (0.15, 95% confidence interval: 0.10 to 0.19), canine distemper virus (0.06, 95% confidence interval: 0.03 to 0.09), and canine pneumovirus (0.05, 95% confidence interval: 0.03 to 0.08) than client‐owned dogs. Odds ratios for M. cynos (0.31, 95% confidence interval: 0.08 to 0.92) and canine respiratory coronavirus (0.05, 95% confidence interval: 0.01 to 0.18) were significantly different between client‐owned and shelter dogs.In all cases except for canine herpesvirus type 1, dogs within the shelter population were observed to be at higher risk of exhibiting asymptomatic carriage of a respiratory pathogen as compared to client‐owned dogs. The strength of this association was strongest for M. cynos and canine respiratory coronavirus.Clinical SignificanceThe risk of canine infectious respiratory disease pathogen exposure posed by asymptomatic client‐owned dogs is poorly defined. This study also corroborates previous reports of high canine infectious respiratory disease prevalence among clinically healthy shelter dogs, and further determined that the overall prevalence of canine infectious respiratory disease pathogen carriage among clinically healthy client‐owned dogs is low but is highest for the traditional pathogen B. bronchiseptica and the emerging pathogen M. cynos.