An acute obstruction of the breathing circuit during surgery can be a devastating situation. A 45-year old man who diagnosed with infective endocarditis and aortic valve regurgitation underwent emergency cardiac surgery. However, an obstruction of the breathing circuit occurred when the cardiopulmonary bypass was weaned. Fortunately, the ventilation normalized after removing the airway filter/heat and moisture exchanger (HME). We report this case of a HME obstruction of the breathing circuit with a review of the relevant literature.