We report the case of a patient in whom brain death was suspected and associated with atelectasis and moderate to severe hypoxemia even though the patient was subjected to protective ventilation, a closed tracheal suction system, positive end-expiratory pressure, and recruitment maneuvers. Faced with the failure to obtain an adequate partial pressure of oxygen for the apnea test, we elected to place the patient in a prone position, use higher positive end-expiratory pressure, perform a new recruitment maneuver, and ventilate with a higher tidal volume (8mL/kg) without exceeding the plateau pressure of 30cmH2O. The apnea test was performed with the patient in a prone position, with continuous positive airway pressure coupled with a T-piece. The delay in diagnosis was 10 hours, and organ donation was not possible due to circulatory arrest. This report demonstrates the difficulties in obtaining higher levels of the partial pressure of oxygen for the apnea test. The delays in the diagnosis of brain death and in the organ donation process are discussed, as well as potential strategies to optimize the partial pressure of oxygen to perform the apnea test according to the current recommendations.