The aim of this study was to investigate whether initial equine bronchoalveolar lavage fluid (BALF) aliquots were more representative of bronchial cytology that bronchiolar and alveolar cytology. Cell viability and total nucleated (TCC), differential (DCC) and absolute cell counts of cytocentrifuged preparations of 3 sequentially collected BALF aliquots (Aliquots 1-3) were compared with those of pooled BALF (Aliquot 4) to assess whether all aliquots were representative of the lavaged lung segment. BALF samples (n = 21) were collected from control horses (n = 5) or heaves-affected horses (n = 5). There were nonsignificant trends of increasing TCC and absolute macrophage count from Aliquot 1 to Aliquot 3 and significant differences in macrophage (P<0.05) and lymphocyte (P<0.01) DCC among aliquots of all horses; however, no linear trend in this DCC data was observed. There was a significant decrease in mast cell DCC (P<0.01) from Aliquot 1 to Aliquot 3 in control horses. Cell viability did not differ significantly among aliquots. There was no diagnostically significant difference in TCC, DCC, absolute cell counts or cell viability, among sequential and pooled BALF aliquots and, therefore, all aliquots can be considered to represent the cytology of the lavaged lung segment. This indicates that even if BALF recoveries are very low, cytological analysis of samples will be of diagnostic value.