Dr. Susan Phillips conducted the autopsy on September 15, 1994, with Swartz present as an observer. The autopsy report was completed on November 29, 1994. The autopsy made two important discoveries. The first discovery was that both of Marietess's superior vena cavas had been narrowed by the purse-string sutures that Odim employed when cannulating. The narrowing was more severe at the superior vena cava on the left (into which the left jugular vein drained) than at the superior vena cava on the right.

The second discovery was of a fresh clot or hematoma surrounding her left pulmonary artery and the hilum of the left lung. The hilum is the area where airways, blood and lymphatic vessels and nerves enter or leave the lungs. Phillips wrote that these two factors were the likely cause of the poor blood flow to Marietess's lungs, particularly on the left side. The narrowing of the superior vena cavas would have reduced blood flow to the heart. In the same way, the hematoma would have pressed on the pulmonary artery and also reduced blood flow to the heart.

Taylor believed that the clot likely arose from the removal of the Blalock-Taussig shunt. Soder testified that he believed it was likely that the clot did not form until the post-operative period, since Marietess was treated with anti-clotting agents during the operation. He also said that it was likely that it did not cause the high pressures noted immediately after surgery, since blood could still flow into the right lung if entry to the left lung were blocked by the clot.