Endoscopy, including bronchoalveolar lavage (BAL) fluid cytology, are invaluable tools for equine lower airway diagnostics. Objectives of the study were to evaluate the reliability of two staining methods, May–Grünwald–Giemsa (MGG) and toluidine blue (TB), for the evaluation of mast cells in cytospin smears from BAL fluid samples and the reliability of a 500-cell differential cell count using both staining methods. Endoscopies and BAL fluid sampling were performed and BAL cytology was evaluated from cytospin smears. BAL cytology slides from 78 horses were evaluated. Three experienced observers evaluated the BAL cytology cytospin smears for the mast cell comparison study. The intra- and interobserver agreements were calculated using intraclass correlation coefficients (ICC). BAL cytology mast cell counts were significantly higher with the TB staining method compared with the MGG staining method. Observer agreements showed below acceptable agreement between observers for mast cell counts for both staining methods, even with fixed coordinates. Based on results from this study recommendation for BAL cytology staining would be to use both the MGG and the TB staining method, relying on the TB for the enumeration of mast cells.