He first studied immunology at Imperial College, London after which he qualified in Medicine at St. Bartholomew's Hospital, London, and subsequently held a research registrar post at Oxford University, where he chose to specialize in inflammatory eye diseases and corneal and cataract surgery. Professor Ayliffe then trained in clinical ophthalmology in Bristol, Manchester, and Harvard, USA.
His doctorate research focused on mechanisms of corneal transplant failure. He went on to win the prestigious Wix Prize for the History of Medicine and the Kabi-Pharmacia Prize for immunological mechanisms of corneal transplant rejection.
Professor Ayliffe has developed a local and tertiary referral service for cornea, uveitis and inflammatory eye disease. He is a Reviewer for a number of professional journals including Eye, British Journal of Ophthalmology and Journal of Cataract and Refractive Surgery. He has undertaken wide media and TV work for national press, the BBC and Channel 4, has an extensive range of publications and has delivered prestigious lectures all over the world. He is also an Examiner for the Royal College of Ophthalmologists and an Advisor to the UK Transplant Service.
As well as a practicing clinician and teacher, Professor Ayliffe also continues to carry out clinical research for the prevention of blindness. He has worked in several developing countries as well as ORBIS, the international flying eye hospital.