Kirklin retired in 1989. He died, aged 86, on April 21, 2004 following a head injury. During Kirklin's lifetime, almost one million heart operations had been performed around the world using the heart-lung bypass machine. The John W. Kirklin Award for Professional Excellence is awarded by the American Association of Surgical Physician Assistants. Among the awards and honours that Kirklin received are:  Between 1978 and 1979, he was president of the American Association for Thoracic Surgery. In addition, he received honorary degrees from a number of universities including the University of Munich, UAB, Indiana University, University of Bordeau and the University of Marseille. Kirklin had more than 700 publications to his name and with his colleague, Brian Barratt-Boyes, he authored the textbook "Cardiac Surgery".