Seasonal changes affect the concentration of dust particles and aeroallergens in the equine stable environment and are hypothesized to change airway cytology in healthy stabled horses. The objective of the study was to evaluate if seasonal changes from May to November influenced the lower airway health cytological findings in clinically healthy stabled horses. Endoscopic examination, including tracheal aspiration (TA) and bronchoalveolar lavage (BAL) cytology was performed in November and May on 63 clinically healthy stabled Danish Warmblood geldings, aged 12.9 (±4.6) years. Tracheal aspiration and BAL cytology were evaluated via May-Grünwald-Giemsa stain after cytocentrifugation of samples. Five-hundred cells were identified microscopically as macrophages, lymphocytes, neutrophils, eosinophils, or mast cells. A significant difference in climatic conditions with lower temperatures (P < .001), fewer sunlight hours (P = .004), less precipitation (P = .006), and higher humidity (P < .001) was found in November compared to May. A significantly higher percentage of neutrophils (Median 6.10%, Quartiles 4.00–8.80, P < .001) and a higher tracheal mucus score (Median 3.50%, Quartiles 1.95–5.20, P = .010) were found during November compared to May period. Furthermore, a positive correlation between TA and BAL neutrophils was found for both sampling times. Mild winter weather conditions with lower temperatures, fewer minutes of sunlight, and a higher percent humidity were associated with significantly higher BAL neutrophil percentage and significantly higher mucus score in stabled clinical healthy horses. The clear seasonal influence on BAL neutrophilia and tracheal mucous findings in clinically normal horse needs to be included in the working diagnosis of asthma in horses.