1. _Exercitationes Apologeticæ pro Divina Gratia._ Amstelodami, 12mo, 1636. Franekeræ, 1651.
2. _A Peaceable and Temperate Plea for Paul's Presbytery in Scotland._ London, 4to, 1642.
3. _A Sermon before the House of Commons, on_ Daniel vi. 26. London, 4to, 1644.
4. _A Sermon before the House of Lords, on_ Luke vii. 22; Mark iv. 38; Matt. viii. 26. London, 4to, 1645.
5. _"Lex Rex:" The Law and the Prince._ London, 4to, 1644. In Fullarton's _Scottish Nation_, 1862, mention is made of another work which is in reality the same as this; on _Civil Polity_. London, 4to, 1657. It is not, however, a separate work, but merely one of the editions of the well-known _Lex Rex_--the edition of 1657, which has the following title:--_Lex Rex; a Treatise of Civil Polity; being a Resolution of Forty-three Questions concerning Prerogative, Right, and Privilege, in reference to the Supreme Prince and People_. The change in the title was a device of the printer, in order to elude the Government, who sought to suppress the book.
6. _The Due Right of Presbyteries._ London, 4to, 1644.
7. _The Trial and Triumph of Faith._ London, 4to, 1645.
8. _The Divine Right of Church Government and Excommunication._ London, 4to, 1646. Appended to this is _A Dispute touching Scandal and Christian Liberty_.
9. _Christ Dying and Drawing Sinners to Himself._ London, 4to, 1647.
10. _A Survey of the Spiritual Antichrist._ London, 1648. To which is appended, _A Modest Survey of the Secrets of Antinomianism_.
11. _A Free Disputation against Pretended Liberty of Conscience._ London, 4to, 1649.
12. _The Last and Heavenly Speeches of John Gordon, Viscount Kenmure._ Edinburgh, 4to, 1649.
13. _Disputatio Scholastica de Divina Providentia._ Edinburgh, 4to, 1651.
14. _The Covenant of Life Opened._ Edinburgh, 4to, 1655.
15. _A Survey of Mr. Hooker's Church Discipline; or, A Survey of the Survey of that Summe of Discipline penned by Mr. Thomas Hooker._ London, 4to, 1658.
16. _Influences of the Life of Grace._ The last work published in his lifetime. London, 4to, 1659. The original title page adds:--"_A Practical Treatise concerning the way, manner, and means of having and improving spiritual dispositions and quickening influences from Christ, the Resurrection and the Life._"