This study aimed to determine if exercise increases the frequency of selected respiratory viruses/bacteria shedding in non-clinical horses using nose wipes. Nose wipes were taken pre- and post- exercise from 133 healthy horses of various ages and disciplines. Wipes were assayed for the presence of selected common (equine herpesvirus-1 (EHV), EHV-4, S. equi spp equi) and commensal (EHV-2, EHV-5, S. equi spp zooepidemicus) respiratory pathogens. The frequency of detection increased significantly (p <
0.05) in the post-exercise wipes for EHV-1, EHV-2, EHV-5, and S. zooepidemicus. EHV-4 and S. equi were only detected in a small number of horses post-exercise. The absolute quantitation of pathogens was significantly lower post-exercise (p <
0.05) for EHV-2, EHV-5, and S. zooepidemicus. While exercise increased the detection rate of EHV-1, EHV-2, EHV-5 and S. zooepidemicus in nose wipes, absolute quantitation of the respective microbes was lower. The use of nose wipes post-exercise to assess the shedding status of selected respiratory viruses/bacteria in non-clinical horses may be an alternative to the more invasive nasal swabs.