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 Cromwell for having encouraged him and others to complete the great Polyglot Bible, but he showed his characteristic moderation by calling attention in the same speech to the pitiable plight of the clergy of the church of England. At the Restoration he offered to resign his mastership to Spurstow, its former holder, but the offer was declined, and Sheldon, archbishop of Canterbury, in recognition of Lightfoot's learning, confirmed him in both the mastership and his living. He took part in the Savoy conference of 1661, siding with the presbyterians. When the Act of Uniformity came into force in 1662 he complied with it, though he is said to have been not very scrupulous in fulfilling its provisions. On 22 Jan. 1667–8 he was appointed to a prebend at Ely, and he died there 6 Dec. 1675. He was buried three days later at Munden.

Lightfoot married, first, in 1628, Joyce (d. 1656), daughter of William Compton of Stone Park, and widow of George Copwood; and, secondly, Anne (d. 1666), widow of Austin Brograve, esq., apparently son of Simeon Brograve of Hamells, Hertfordshire. By his first wife alone he had issue, viz. four sons and two daughters. Of the sons, John was chaplain to Bryan Walton, bishop of Chester; Anastasius Cottonus Jacksonus—the two latter names commemorated Lightfoot's friends, Sir Rowland Cotton, and Sir John Jackson—became vicar of Thundridge, Hertfordshire, 25 June 1661; Anastasius was a London tradesman, and Thomas died young. Of the daughters, Joyce married, on 8 Jan. 1655–6, John Duckfield, rector of Aspeden, Hertfordshire; and Sarah became wife of a Staffordshire gentleman named Colclough.

He bequeathed his oriental books to Harvard College in America, where they were burnt in 1769. Many of his papers passed to his son-in-law, Duckfield, who communicated them to John Strype.

Lightfoot holds a very high rank among Hebrew scholars. His rabbinical learning was very wide, and, according to Gibbon, he, ‘by constant reading of the rabbis, became almost a rabbi himself.’ He set himself to illustrate from Talmudical and like authorities the phraseology of the Old Testament, and to explain the customs mentioned both there and in the New Testament. To him is ascribed the credit of opening to the modern world ‘the fountains of Talmudical learning.’ Schoettgen, a German scholar who followed half a century later the same line of study, wrote, ‘Nisi Lightfootus lyrasset, multi non saltassent.’ Dr. Adam Clarke considered Lightfoot to be the first of all English writers in biblical criticism as regards learning, judgment, and usefulness. In his own day his eminence as a Hebrew scholar was recognised abroad, and Frederic Miege, Theodore Haak, J. H. Otho of Berne, Knorr, the Silesian cabbalistic scholar, and the younger Buxtorf, were among his correspondents or visitors. Publishers, however, he complained to Buxtorf, would rarely undertake to print his works at their own risk. Most of them appeared at his own expense.

Among his chief works were: ‘Harmony of the iv Evangelists among themselves and with the Old Testament, with an explanation of the chiefest difficulties both in language and sense,’ pt. i. London, 1644, 4to; pt. ii. London, 1647, 4to; pt. iii. London, 1650, 4to; ‘Harmony, Chronicle, and Order of the Old Testament,’ London, 1647, and of the New Testament, London, 1655, with a discourse on the ‘Fall of Jerusalem.’ But Lightfoot is mainly remembered by a series of volumes entitled ‘Horæ Hebraicæ et Talmudicæ,’ of which the earliest, ‘impensæ I. in chronographiam aliquam Terræ Israeliticæ; II. in Evangelium S. Matthæi,’ appeared at Cambridge in 1658, 4to, dedicated to the students of Catharine Hall, and was followed by similar studies ‘In Evangel. Marci’ with ‘Decas Chorographica’ (Cambridge, 1663, 4to), dedicated to Charles II; ‘In Epistolam S. Pauli ad Corinthios’ (Cambridge, 1664, Paris 1677, Amsterdam 1677, and Leipzig 1679), dedicated to Sir William Morice; ‘In Evangel. Johannis,’ with ‘Disquisitio Chorographica’ (London, 1671, 4to), dedicated to Sir Orlando Bridgman; ‘In Evangel. S. Lucæ,’ with ‘Chorographia pauca’ (Cambridge, 1674, 4to), dedicated to Archbishop Sheldon; and posthumously—‘In Acta Apostolorum et in Epistolam S. Pauli ad Romanos’ (London, 1678, 4to), prepared for the press by [q. v.] The ‘Horæ’ on the Four Evangelists, together with the chorographical essays, were edited by the Hebrew scholar Carpzov at Leipzig (1675 and 1684), and those on the Acts, Romans, and Corinthians by the same editor, Leipzig, 1679. Schoettgen reprinted the greater part of Lightfoot's ‘Horæ’ in his own ‘Horæ Hebraicæ et Talmudicæ in universum Novum Testamentum,’ 1733, 4to. An edition of the whole, in an English version, was edited by [q. v.] in 1859 (4 vols.)

Lightfoot's other works, apart from sermons, published in 1643 (two), 1645 (two), and 1647 were:  ‘A Few and New Observations on the Book of Genesis, the most of them certain, the rest probable, all harmless, strange, and rarely heard of before,’ London, 1642.  ‘A Handful of Gleanings out of the Book of Exodus,’ London, 1643, 