Wilkinson qualified in medicine in 1976 from the University of London. He held resident appointments in London, coming to Manchester in 1978 on a rotational training scheme in surgery. In 1982 he was appointed research fellow to the department of medical oncology at Christie Hospital Manchester and surgical registrar at Withington Hospital Manchester. Wilkinson was later consulting surgeon to Bolton Infirmary. He was a fellow of the Royal Society of Medicine and the Association of Surgeons.
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