Fungi detection in equine airways may be performed on either tracheal wash (TW) or bronchoalveolar lavage fluid (BALF) by either cytology or culture. However, method comparisons are sparse. The objective was to determine the prevalence of fungi in airways of horses with or without respiratory clinical signs, according to the sample site and laboratory methodology. Sixty-two adult horses, investigated in the field or referred for respiratory disease, were included.TW and BALF were collected from each lung separately through a videoendoscope. Fungi were detected by cytology and culture. Overall prevalence of fungi was of 91.9% in TW and 37.1% in BALF. Fungi were positively cultured from 82.3% TW and 20.9% BALF. Fungal elements were observed by cytology in 69.4% TW and 22.6% BALF. Prevalence of fungi was not significantly different between horses with or without clinical signs. In 50%of horses, the same fungi were detected in both TW and hay, but fungi detected in BALF and hay did not correspond for any horse. Poor agreement was found between TW and BALF and between culture and cytology (Cohen’s kappa coefficient (κ) < .20). Moderate agreement was found between cytology of left/right lungs (κ = .47). The prevalence of fungi by cytology on pooled BALF was significantly different (p = .023) than on combined left + right BALF. A high prevalence of fungi was detected in the lower respiratory tract of horses, particularly in the TW. Hay might not be the primary source of fungi of the lower respiratory tract of horses.

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