Background: Respiratory conditions are the leading cause of training disruption in racing horses. Molecular approaches to diagnose respiratory viruses have provided an opportunity for early and subclinical pathogen detection, particularly in samples from the upper respiratory tract. Gammaherpesvius (EHV-2 and EHV-5) have variable presentations in horses. However, the infection can be asymptomatic and act as a co-factor for the development of other diseases. In this descriptive observational study, 10 healthy, young horses at regular training in Southern Brazil underwent clinical examination, videoendoscopy of the respiratory system, cytological evaluation of TA (tracheal aspirate) and BALF (bronchoalveolar lavage fluid), along with qPCR, in order to evaluate the presence of EHV-2 and EHV-5 in lower respiratory tract samples and compare with correspondent cytological and endoscopical findings. Results: At least one abnormality per horse during endoscopy examination was observed, including, but not limited to, mucous secretion in the airways and pharyngeal lymphoid hyperplasia. The presence of EHV-2 and EHV-5 was detected by qPCR in three out of ten animals. One horse was positive for EHV-2 alone, one for EHV-5 alone, and one was positive for both viruses. No videoendoscopic finding correlated with each other neither predicts gammaherpesvirus status (positive or negative test). Additionally, there was no relationship between the percentage of cells in both TA and BALF and the probability to test positive for herpesvirus.Conclusions: To the authors’ knowledge, this is the first molecular detection of EHV-2 and 5 in Brazilian Thoroughbred horses. These findings may provide new insights into the epidemiological situation of EHV-2 and 5 in Brazilian athletic young horses, evidencing the importance of the molecular investigation, early detection, and prevention of respiratory diseases.