[1] Clarke's altered, Nontrinitarian revision of the 1662 Book of Common Prayer continues to influence worship among modern Unitarians.

[3][4] His tutor at Caius was John Ellis, a personal friend of Isaac Newton, but who in natural philosophy taught in line with the Cartesianism that prevailed in the university.

The Newtonian theologians used the Boyle Lectures to attack opponents (Thomas Hobbes and Baruch Spinoza, deists and freethinkers in particular).

[12] Clarke's reputation rested largely on his effort to demonstrate the existence of God, and his theory of the foundation of rectitude.

[13] The public correspondence of Samuel Clarke with the English freethinker Anthony Collins in 1707 and 1708 was a debate on the nature of consciousness.

[15] By the sixth edition (1731), Clarke's own Letter to Mr Dodwell of 1706 had grown to 475 pages, including the replies of Collins.

He took the degree of doctor in divinity in 1710,[4] defending as his thesis the two propositions: Nullum fidei Christianae dogma, in Sacris Scripturis traditum, est rectae rationi dissentaneum [No doctrine of the Christian faith, delivered in the Holy Scriptures, is contrary to right reason.

], and Sine actionum humanarum libertate nulla potest esse religio [Without the freedom of human actions, there can be no religion.].

[5] Clarke was required to swear to keep the 39 Articles; and his attempt at self-justification by putting his views in book form were not immediately successful.

He was reacting to issues that had been raised elsewhere in Europe, by Petavius, by Christopher Sandius and Daniel Zwicker for the Socinian camp, and the Arminians.

[24] It was only with the close discussions of Clarke and his major opponent Daniel Waterland, a generation later, that the theological and historical points involved came clearly into focus.

[25] Waterland argued in theology for the Anglican orthodoxy of time, in particular that the possible attitudes were, besides the orthodox Athanasian view, limited to Arianism and Sabellianism; and that the two latter were not consistent with Scripture.

[25] By summer 1714 the debate on The Scripture Doctrine of the Trinity had ramified, and provoked a formal complaint from the Lower House of Convocation: the Blasphemy Act 1697 still made it an offence for "any person, educated in or having made profession of the Christian religion, by writing, preaching, teaching or advised speaking, to deny the Holy Trinity".

[25] Caroline of Ansbach, the Princess of Wales, requested that Clarke defend his views in a disputation with Edward Hawarden, and it took place in 1719, in her presence.

[31][32] That year, Clarke privately altered his copy of the 1662 Book of Common Prayer, deleting Trinitarian formulae and the Athanasian Creed.

[35][36] Lindsey, using Clarke's work as his basis, published his own Unitarian prayer book revision in 1774 and began using it with his Essex Street Chapel congregation.

[37] In 1785, Lindsey's work was further adapted by James Freeman for use at King's Chapel in Boston, where a ninth edition version is still used.

In 1727, on the death of Sir Isaac Newton, he was offered by the court the post of Master of the Mint, worth on an average from £1200 to £1500 a year.

In 1712 he published an annotated edition of Caesar's Commentaries, with engravings, dedicated to John Churchill, 1st Duke of Marlborough.

[9] In 1699 Clarke published two treatises: Three Practical Essays on Baptism, Confirmation and Repentance and Some Reflections on that part of a book called Amyntor, or a Defence of Milton's Life, which relates to the Writings of the Primitive Fathers, and the Canon of the New Testament.

In 1728 was published "A Letter from Dr Clarke to Benjamin Hoadly, F.R.S., occasioned by the controversy relating to the Proportion of Velocity and Force in Bodies in Motion," printed in the Philosophical Transactions.

[9] Soon after his death his brother, Dr John Clarke, published, from his original manuscripts, An Exposition of the Church Catechism, and ten volumes of sermons.

These became the source of Theophilus Lindsey's The Book of Common Prayer Reformed According to the Plan of the Late Dr. Samuel Clarke 1774, and other liturgical works.