After leaving the PGA Tour, Mallon returned to Duke University to study medicine graduating as an M.D. in 1984. He was a resident at Duke University medical center between 1984 and 1990 and is now the Associate Consulting Professor of Orthopaedics as well as having his own practice. Mallon specializes in complex reconstructive shoulder and elbow surgery and is a fellow of the American Academy of Orthopaedic Surgeons, a member of the American Shoulder and Elbow Surgeons, where he served as vice-president in 2012 and will be president in 2014, and a member of the advisory council of the Institute of Preventative Sports Medicine. He has written widely on the subject of sporting injuries and has been the medical editor of Golf Digest since 1987. Mallon was previously the North American editor of the Journal of Shoulder and Elbow Surgery.
Who's Who der Olympischen Spiele 1896–1992. Agon-Sportverlag Kassel 1992 ISBN3-928562-47-9 (with Erich Kamper)
The Golf Doctor : How to Play a Better, Healthier Round of Golf. Macmillan. 1996. ISBN0-02-860853-4 (with Larry Dennis).
Historical Dictionary of the Olympic Movement. Scarecrow Press. 1996. ISBN0-8108-3062-0 (with Ian Buchanan)
The 1896 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 1997. ISBN0-7864-0379-9 (with Ture Widlund).
The 1900 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 1997. ISBN0-7864-0378-0.
The 1904 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 1999. ISBN0-7864-0550-3.
The 1906 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 1999. ISBN0-7864-0551-1.
The 1908 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 2000. ISBN0-7864-0598-8. (with Ian Buchanan)
The 1912 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 2001. ISBN0-7864-1047-7. (with Ture Widlund)
The 1920 Olympic Games: Results for All Competitors in All Events. With Commentary. McFarland & Company, Jefferson (North Carolina) 2003. ISBN0-7864-1280-1. (with Anthony Bijkerk)
Orthopaedics for the House Officer. Williams and Wilkins 2000 (with McNamara and Urbaniuk)
Ernest Amory Codman: The End Result of a Life in Medicine. WB Saunders 1999