Born in Connington, Huntingdonshire, he was educated at Westminster School and Jesus College, Cambridge. He moved to 'Cotton House', Westminster, which stood on the site of the present House of Lords, and began to amass the extraordinary collection of manuscripts for which he is now known; he also collected coins. Scholars (including Bacon, Camden, Speed, Ralegh, Selden, Ussher - and Jonson ) were freely given access to his library. He collaborated with Camden on some of his historical works, but published little independently, although he did write many papers for the Royal Society of Antiquaries. He was knighted in 1603, became MP for Huntingdon in 1604, and created a baronet in 1611. In 1615-16 he altered papers implicating his friend and patron the earl of Somerset in the Overbury scandal, and he was imprisoned in the Tower for several months. He became an MP again in 1624, 1625 and 1628-9, and quickly became known as a member of the Parliamentary party of Sir John Eliot, in which cause he published his tracts The History of Henry III (1627) and Dangers wherein the kingdom now standeth (1628). As a result of his political activism he was excluded from his own library by Charles I from 1629 until his death. The library was eventually gifted to the nation in 1702, and was transferred to the British Museum (now the British Library) in 1753, where its shelfmarks are still those of Cotton's original organisation into fourteen cases, each named for the Roman emperor whose bust decorated it.