Professor Sir Mark Pepys was elected to an Honorary Fellowship of Trinity College, Cambridge, in 2014.
Professor Sir Mark Pepys received a knighthood for services to biomedicine in the 2012 New Year Honours list.
Professor Pepys was awarded the 2008 Ernst Chain Prize. The Ernst Chain prize was established by Imperial College London in 2003 in honour of Sir Ernst Chain, who received the 1945 Nobel Prize in Physiology or Medicine with Sir Alexander Fleming and Sir Howard Florey for the discovery of penicillin and its curative effect in various infectious diseases. It is awarded annually to a scientist who has made an original and substantive contribution to the field of science which has furthered, or is likely to further, understanding or management of human diseases. Professor Pepys delivered a lecture entitled 'Towards curing amyloidosis' and received his award of a commemorative medal and £10,000 on Wednesday 12 March at Imperial College London.
Professor Pepys was the Harveian Orator of the Royal College of Physicians for 2007. The Oration entitled 'Science and serendipity' was delivered on 18 October 2007, 351 years after Harvey's donation to the College which he instructed in 1656 should support a lecture encouraging Fellows and Members of the College "to search and study out the secret of nature by way of experiment".
Professor Pepys was awarded the Royal Society's GlaxoSmithKline Prize and Lecture for 2007. This award is for original contributions to medical and veterinary sciences published within ten years from the date of the award. The prize, established initially by means of a donation from The Wellcome Foundation Limited, consists of a gold medal and a gift of £2500 and the recipient is called upon to deliver an evening lecture at the Royal Society. The first award was made in 1980, the centenary year of The Wellcome Foundation, and is awarded biennially. It was renamed the GlaxoSmithKline Prize in 2002. The 2007 Prize was awarded to Professor Mark Pepys FRS, University College London, "for his excellent work as a clinical scientist who has identified specific proteins as new therapeutic targets and developed novel drugs with potential use in amyloidosis, Alzheimer's disease and cardiovascular disease". Professor Pepys delivered his prize lecture entitled "From proteins to drugs" on Thursday April 3 2008 at the Royal Society.