Abstract The objectives of this study were to estimate the prevalence and the potential role of equine herpesviruses (EHVs) detection in both bronchoalveolar lavage (BAL) and tracheal wash (TW). The population included a control group (CTL; 37 TW and 25 BAL) and a pathological group (PAT; 259 TW and 387 BAL), including horses either suffering from respiratory diseases including syndrome of tracheal inflammation, inflammatory airway disease, recurrent airway obstruction, or submitted to respiratory investigation because of exercise intolerance or poor performance. Each respiratory liquid was submitted to a standardised cytological analysis, mentioning the morphological abnormalities of exfoliated epithelial cells (ECAb) and ciliocytophthoria (CCPh) as markers of potential viral infection, as well as PCR assays including a consensus PCR and virus-specific PCR for both equine alphaherpesviruses (EHV-1; EHV-4) and gammaherpesviruses (EHV-2; EHV-5). The EHV infections were more prevalent in the TW of PAT group (P = 0.004), with the highest prevalence being for EHV-2 (P = 0.006). The EHV detection in BALs was not significantly different between groups. The EHVs detection in TW was correlated to the polymorphonuclear neutrophil (PMN) counts in the respiratory liquid but not with CCPh or ECAb. CCPh or ECAb were associated with both consensus PCR and EHV-2 and EHV-5 virus-type PCR in the BAL only. The significant detection of EHVs in the TW of PAT group in association with the PMN increased counts could lead to further investigations about their putative role in equine syndrome of tracheal inflammation.