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Sir Thomas Clayton (c 1612 – 4 October 1693) was an English doctor, academic and politician who sat in the House of Commons in 1660.
Clayton was the son of Thomas Clayton MD of Oxford. He matriculated at Pembroke College, Oxford on 25 May 1627, aged 15 and was awarded BA on 22 January 1629 and MA on 17 October 1631. He was of Gray's Inn in 1633. Further awards from Oxford were B.Med on 18 July 1635 and D.Med on 19 June 1639. He was regius professor of medicine at Oxford from 1647 to 1665.
In 1660, Clayton was elected Member of Parliament for Oxford University in the Convention Parliament. He was knighted on 27 March 1661. From 1661 to 1693 he was warden of Merton College, Oxford.
Clayton was of La Vache, Buckinghamshire. He died at the age of 80.