OBJECTIVESTo determine the prevalence of nine canine infectious respiratory disease (CIRD) pathogens in asymptomatic dogs presented at animal shelters across the United States.METHODSOcular and oronasal swabs from asymptomatic dogs (n= 503) were tested usingqPCRassay forBordetella bronchiseptica, canine adenovirus type 2 (CAV‐2), canine distemper virus (CDV), canine herpesvirus type 1 (CHV), canine influenza virus (CIV), canine parainfluenza virus (CPIV), canine respiratory coronavirus (CRCoV),Mycoplasma cynosandStreptococcus equisubspzooepidemicus.RESULTSA total of 240 (47 · 7%) asymptomatic dogs werePCR‐positive for at least oneCIRDpathogen. Prevalence of two‐, three‐, four‐, and five‐pathogen cases was 12 · 7, 3 · 8, 1 · 8, and 0 · 4%, respectively.Mycoplasma cynos(29 · 2%),B. bronchiseptica(19 · 5%),CAV‐2 (12 · 5%),CDV(7 · 4%) andCPIV(3 · 2%) were the most commonly detected pathogens.CLINICAL SIGNIFICANCEThe prevalence of traditional and newly emerging pathogens associated withCIRDis poorly defined in clinically healthy dogs. This study determined that a high percentage of asymptomatic shelter dogs harborCIRDpathogens, including the newly emerging pathogenM. cynosand the historically prevalent pathogenB. bronchiseptica.