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 is uncertain. Sir Thomas was the intimate friend and correspondent of Sir John Eliot, and was entrusted by his influence with the representation of St. Germans (Eliot's native place) in the third of Charles I's parliaments. He was M.P. for Huntingdon in the short parliament of 1640, but took no active part in politics. Like his father, Sir Thomas gave scholars free access to his library. Dugdale from an early age was very often there, and obtained there much of his material for his ‘Monasticon.’ In 1640 Sir Thomas lent his father's collection of coins to Sir Symond D'Ewes, a loan which the recipient hardly deserved after having written in his autobiography (ii. 43) ‘that Sir Thomas was wholly addicted to the tenacious increasing of his worldly wealth, and altogether unworthy to be master of so inestimable a library.’ Sir Thomas seems to have taken no part in the civil wars, but, knowing the suspicions which his library excited in all political parties, he removed the greater part in 1650 to a villa at Stratton which belonged to his son's wife (, Itin. Curiosum, v. 78;, Magna Brit. i. 87). His house at Westminster was left at the disposal of the parliament, and Charles I slept there during his trial. He died at Connington on 13 May 1662, and was buried with his father. He married, first, Margaret, daughter of William, lord Howard, of Naworth Castle, Cumberland, by whom he had one son, John; second, Alice, daughter and heiress of Sir John Constable of Dromanby, Yorkshire, widow of Edmund Anderson of Stratton and Eyworth, Bedfordshire, by whom he had four sons. (The second son, Robert, was M.P. for Cambridgeshire, was knighted, was commissioner of the post office, and friendly with Evelyn.)

Sir (1621–1701), the eldest son of Sir Thomas by his first wife, showed himself more of a scholar than his father. His letters (1680–90) to his friend, Dr. Thomas Smith, who first catalogued Sir Robert's library, indicate a real love of learning and wide reading. They are interspersed with Latin and Greek quotations, original Latin verses, and criticisms of ancient and modern writers, besides exhibiting deep reverence for his grandfather's memory. In one letter he states that he was engaged on his autobiography (, Letters, i. 20–6). Sir John, who edited two of his grandfather's tracts, added to the library, and allowed Dugdale, who introduced Thomas Blount to his notice, to make whatever use he pleased of it. Evelyn knew him well, and Pepys slightly; the former describes him as ‘a pretended great Grecian, but had by no means the parts or genius of his grandfather’ (Diary, 2 July 1666, ii. 197). By his first wife he became possessor of a villa at Stratton, Bedfordshire, where he lived in his later years. In 1700 Sir John made known his intention of practically giving the Cottonian Library to the nation, but died 12 Sept. 1702, aged 81, before any final arrangements for the public use of the library were made. His portrait was painted by Sir Godfrey Kneller, and has been engraved. Sir John married, first, Dorothy, daughter and heiress of Edmund Anderson of Stratton and Eyworth, Bedfordshire, his stepmother's daughter; and, second, Elizabeth (d. 3 April 1702), daughter of Sir Thomas Honywood of Mark's Hall, Essex. By his first wife he had an only son, John, who died before him in 1681, and by his second wife another son, Robert.

The third baronet's immediate successor was his grandson (son of his elder son), John (1679–1731). He was elected M.P. for Huntingdon in 1705, was unseated on petition, and was M.P. for Huntingdonshire Dec. 1710 to 1713. In 1708 he married Elizabeth (d. 11 Feb. 1721–2), daughter of James Herbert of Kingsey, Oxfordshire, granddaughter of the Duke of Leeds, and died 5 Feb. 1730–1, being buried in Lamb's Conduit Fields. He carried out his grandfather's wishes respecting the library. His uncle Robert (1669–1749) became fifth baronet. He was educated at Trinity College, Cambridge, was twice married, and died 12 July 1749. His son, Sir {{sc|John}, sixth baronet, died without issue on 27 March 1752, and the title became extinct. The sixth baronet was a friend of Dr. Stukeley (, Memoirs, i. 216–20). Connington House was pulled down in 1753.

Meanwhile the Cottonian Library had passed entirely out of the hands of the family. In 1700, in accordance with the wishes of the third baronet, who died in 1702, an act of parliament (12 and 13 Will. III, cap. 7) was passed declaring that ‘Sir John Cotton, in pursuance of the desire and intention of his father and grandfather, is content and willing that his mansion house and library should continue in his family and name, and that it be kept and preserved by the name of the Cottonian Library for public use and advantage.’ In April 1706 Sir Christopher Wren was directed to fit up the library for public use, and reported that Cotton House had fallen into complete decay. William Hanbury, the fourth baronet's brother-in-law, was appointed keeper (June 1706), but soon afterwards Dr. Bentley, the royal librarian, and his deputy, David Casley, claimed full control. In 1707 an act of parliament (6 Anne, cap. 30) recited that, to increase the public utility of the library, Cotton House, with the library and