The mechanism of recurrent airway obstruction (RAO) in horses was investigated by measuring the membrane domain structure and oxy-redoxy activity in phagocytes isolated from bronchoalveolar lavage fluid (BAL) and from the blood of healthy and RAO horses by electron paramagnetic resonance (EPR). Differences in the activity of intracellular antioxidant enzymes CAT, GPx, and SOD measured in phagocytes of RAO horses in comparison to healthy horses showed that the phagocytes were affected by oxidative stress. In comparison with polymorphonuclear leukocytes (phagocytes) from the blood of healthy horses the reduction mechanisms in BAL were faster and coincided with the merging of disordered membrane domains, while in horses with RAO the reduction and membrane domain structure remained unchanged. We assume that the merging of lipid domains observed in phagocytes from BAL of healthy horses could promote cluster formation of membrane proteins or ligands, which could trigger the activation process in phagocytes of healthy horses and consequently the physiological response that probably did not happen in phagocytes of RAO horses.