The earlier material (MSS.3430-3431) consists almost entirely of correspondence of the General Assembly of the Church of Scotland, and includes appointments of Commissioners to the Assembly from 1638 onwards; accounts of the intrusion of ministers into parishes, and similar disputes, 1702-1755; reports on the prevalence of Roman Catholicism, with lists of papists and renunciations of popery, 1703-1751; and correspondence on the supply of books especially to the Highlands, in association with the Society for Promoting Christian Knowledge, 1704-1731. Other subjects include the affairs of the Universities of St Andrews and Edinburgh, and the Infirmary, Edinburgh. Among the correspondents are Hugh Blair (copies of letters), 1795, and the Reverend Alexander Carlyle, Minister of Inveresk, 1786-1799.

The Very Reverend John Lee's own correspondence starts in 1797 and continues until his death in 1859. It relates to the concerns of all the offices which he held, from that of Minister of the Hanover Street Chapel in London to those of Moderator of the General Assembly and Principal of Edinburgh University, and also to the many public affairs in which he took an active interest. Scottish Church and University affairs preponderate. The former include Lee's parochial charges; his life-long dispute with the King's Printers over the printing of Bibles for Scotland from 1822 onwards; his work to improve the status of the Church of Scotland in the Canadas, 1826; Sabbath profanation, from 1832; education in Ireland, 1832-1833; Dr Chalmers's Church Extension Bill, 1836, which occasioned the quarrel between Lee and Chalmers; parochial education, especially in 1838; non-intrusion and the Disruption, from 1842.

There is also much correspondence, 1809-1812, dealing with the share taken by Lee in the production of Sir David Brewster's ‘Edinburgh encyclopaedia’.

Lee's correspondents include many of the more distinguished Church leaders and University dignitaries of the day. In addition there are letters of John Home, Alexander Carlyle, John Leyden, Henry Mackenzie, David Hume, and Dugald Stewart, and many written to Principal Baird on the subject of metrical Psalms by Joanna Baillie, Thomas Campbell, Wordsworth, Southey, Mrs Hemans, and others, 1824-1827.