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 brought him into greater prominence, and in February 1546–7 he entered the service of Protector Somerset, whose brother-in-law, Sir Clement Smith of Little Baddow, Essex [see under, (1534?–1607)], was perhaps a relative of Thomas Smith. The latter was made clerk of the privy council, steward of the stannary court, and master of the court of requests which the Protector set up in his own house to deal with the claims of poor suitors. Smith set out with Somerset on the Scottish expedition (August–September 1547), but was laid up at York with a fever. Before the end of the year he became provost of Eton and dean of Carlisle. On 17 April 1548 he was sworn one of the two principal secretaries of state in succession to Paget, his colleague being Sir [q. v.] In the following June he was sent on a special mission to Flanders, to negotiate for the levy of mercenaries, and to secure as far as possible the support of the emperor in the impending war with France. He reached Brussels on 1 July, but met with little success, and returned in August. In October he was employed in formulating the English claims of feudal suzerainty over Scotland. In the following January he took an active part in the examinations of Sir [q. v.] and, lord Seymour of Sudeley [q. v.] Soon afterwards he was knighted. He was likewise consulted about the reform of the coinage, and advised the prohibition of ‘testons.’ He was a member of the commissions appointed to visit the universities (November 1548), to examine Arians and anabaptists (April 1549), and to deal with Bonner (September 1549). His proceedings on the latter were especially obnoxious to Bonner, who was imprisoned in the Tower for his behaviour to Smith.

Smith remained faithful to the Protector to the last. He was with him at Hampton Court in October, and accompanied him thence to Windsor, where, on the 10th, he was removed from the council and from his post of secretary, and deprived of his professorship at Cambridge. On the 14th he was imprisoned in the Tower, whence he was released on 10 March 1549–50, on acknowledging a debt of 3,000l. to the king. In the same year he was summoned as a witness against Gardiner, and, with Cecil, drew up the articles for the bishop to sign; but he seems to have used his influence in Gardiner's favour, a service which Gardiner repaid under Mary's reign. In May 1551 Smith accompanied Northampton on his embassy to the French court. He returned in August, and in October was placed on a commission to ‘rough-hew the canon law.’ But for the most part he lived at Eton, where his relations with the fellows were somewhat strained. Early in 1552 he was summoned before the council to answer their complaints; but in the following autumn Northumberland and his principal adherents dined with Smith at Eton and decided the dispute in his favour. In October he was selected to discuss with the French commissioners the claims for compensation on the part of French merchants.

In August 1553, a month after Mary's accession, Smith was summoned before the queen's commissioners, but Gardiner's friendship secured him from molestation, and he even obtained an indulgence from the pope (, p. 47). On 8 Sept. he was returned to parliament as member for Grampound, Cornwall. In the following year, however, he resigned the provostship of Eton and deanery of Carlisle quasi sponte, as he says himself, and perhaps in order to marry his second wife. For the remainder of Mary's reign he lived in retirement, busy with his studies and building. The accession of Elizabeth once more brought him public employment. On 22 Dec. 1558 he was placed on a commission ‘for the consideration of things necessary for a parliament,’ and on 6 Jan. 1558–9 was elected member for Liverpool. He was also a member of the ecclesiastical commission to revise the Book of Common Prayer, which met at his house in Cannon Row, Westminster. In the following year he was in attendance on John, duke of Friesland, son of the king of Sweden, during his visit to England, and in 1560 wrote a dialogue on the question of the queen's marriage, which is extant in Addit. MS. 4149, Ashmole MS. 829, and Cambr. Univ. MS. Gg. 3, and is printed in the Appendix to his life by Strype (pp. 184–259).

In September 1562 Smith was sent ambassador to France, a post of great difficulty and some danger, owing to the civil war between the Guises and the Huguenots. Elizabeth had decided to help the latter and herself at the same time by seizing Havre, and Smith's position at Paris was threatened by the Guise party. From 28 Aug. to 17 Sept. 1563 he was even imprisoned at Melun. His task was rendered more difficult by the retention of Sir [q. v.] as joint ambassador, and the lack of confidence with which the two were treated by Elizabeth, coupled with mutual jealousy, led on one occasion to a violent outbreak between them (Lettres de Catherine de Médicis, ii. 171;, Rise of the Huguenots, ii. 128). At length, on 12 April 1564,