Cytology of bronchoalveolar lavage fluid (BALF) from one lung may not predict findings in the contralateral lung of the same horse. The aim of this study was to determine whether a pooled BALF from both lungs was representative of corresponding individual samples. Fifty-one horses referred for poor performance and/or respiratory signs and for which a BALF was collected from both lungs, were included in the study. Cytology of pooled and individual BALF samples were performed using a masked protocol. Based on clinical signs and individual BALF cytologies, horses were classified as control (CTL), mild equine asthma (mEA), severe equine asthma (sEA) and/or exercise-induced pulmonary haemorrhage (EIPH). No significant difference was observed between pooled and individual BALF samples for all cell types (P>0.05). Correlations between pooled and individual BALF samples were good (r≥0.9) for neutrophil proportions and haemosiderophages/macrophages ratio, and moderate (r≥0.4) for metachromatic cell and eosinophil proportions. Similarly, intraclass correlation coefficient (ICC) were good (ICC≥0.9) for neutrophil proportions and haemosiderophages/macrophages ratio and substantial (ICC≥0.6) for metachromatic cell proportions. Based on threshold values for pooled samples as determined by receiver operating characteristic (ROC) analysis, categorical agreements were good (κ≥0.97) for diagnosis of mEA/sEA, and substantial (κ=0.74) for EIPH. Using a pooled BALF sample, only one horse was incorrectly classified as CTL instead of mEA and three horses were classified as EIPH instead of CTL. In conclusion, BALF cytology from pooled sample is representative of both individual lungs, and constitutes a valid method to diagnose EA.