[8] Ordained in 1599[9][10] and elected to a college fellowship by 1600,[11] Cudworth Snr was much influenced by William Perkins, whom he succeeded, in 1602, as Lecturer of the Parish Church of St Andrew the Great, Cambridge.

[15] Lord Rich presented him to the Vicariate of Coggeshall, Essex (1606)[16] to replace the deprived minister Thomas Stoughton, but he resigned this position (March 1608), and was licensed to preach from the pulpit by the Chancellor and Scholars of the University of Cambridge (November 1609).

[20] His marriage (1611) to Mary Machell (c.1582–1634), (who had been "nutrix" – nurse, or preceptor – to Henry Frederick, Prince of Wales)[21] brought important connections.

[22] Mary's mother (or aunt) was the sister of Sir Edward Lewknor, a central figure (with the Jermyn and Heigham families) among the puritan East Anglian gentry, whose children had attended Emmanuel College.

[23] Mary's Lewknor and Machell connections with the Rich family included her first cousins Sir Nathaniel Rich and his sister Dame Margaret Wroth, wife of Sir Thomas Wroth of Petherton Park near Bridgwater, Somerset, influential promoters of colonial enterprise (and later of nonconformist emigration) in New England.

[24] Cudworth continued to study, working on a complete survey of Case-Divinity, The Cases of Conscience in Family, Church and Commonwealth while suffering from the agueish climate at Aller.

[27] Ralph Snr died at Aller declaring a nuncupative will (7 August 1624) before Anthony Earbury and Dame Margaret Wroth.

He published a tract entitled The Union of Christ and the Church, in a Shadow (1642),[44] and another, A Discourse concerning the True Notion of the Lord's Supper (1642),[45] in which his readings of Karaite manuscripts (stimulated by meetings with Johann Stephan Rittangel) were influential.

[46] Following sustained correspondence with John Selden[47] (to whom he supplied Karaite literature), he was elected (aged 28) as 11th Regius Professor of Hebrew (1645).

[62][63] During 1657, Cudworth advised Bulstrode Whitelocke's sub-committee of the Parliamentary "Grand Committee for Religion" on the accuracy of editions of the English Bible.

[64] Cudworth was appointed Vicar of Great Wilbraham, and Rector of Toft, Cambridgeshire Ely diocese (1656), but surrendered these livings (1661 and 1662, respectively) when he was presented, by Dr Gilbert Sheldon, Bishop of London, to the Hertfordshire Rectory of Ashwell (1 December 1662).

He first analysed four forms of atheism from ancient times to present, and showed that all misunderstood the principle of life and knowledge, which involved unsentient activity and self-consciousness, addressing the tension between theism and atheism, took both the Stoic idea of Divine Reason poured into the world, and the Platonic idea of the world soul (anima mundi) to posit a power that was polaric – "either as a ruling but separate mind or as an informing vital principle – either nous hypercosmios or nous enkosmios.

[92] All of the atheistic approaches posited nature as unconscious, which for Cudworth was ontologically unsupportable, as a principle that was supposed to be the ultimate source of life and meaning could only be itself self-conscious and knowledgeable, that is, rational, otherwise creation or nature degenerates into inert matter set in motion by random external forces (Coleridge's 'chance whirlings of unproductive particles').

Cudworth saw nature as a vegetative power endowed with plastic (forming) and spermatic (generative) forces, but one with Mind, or a self-conscious knowledge.

Cudworth argued that materialism/mechanism reduced "substance to a corporeal entity, its activity to causal determinism, and each single thing to fleeting appearances in a system dominated by material necessity.

"[95] Cudworth's works included The Union of Christ and the Church, in a Shadow (1642); A Sermon preached before the House of Commons (1647); and A Discourse concerning the True Notion of the Lord's Supper (1670).

Both this and the Treatise on eternal and immutable Morality are connected with the design of his magnum opus, The True Intellectual System of the Universe.

[98] In 1678, Cudworth published The True Intellectual System of the Universe: the first part, wherein all the reason and philosophy of atheism is confuted and its impossibility demonstrated, which had been given an Imprimatur for publication (29 May 1671).

[97] Enlarging his plan, he proposed to prove three matters: These three comprise, collectively, the intellectual (as opposed to the physical) system of the universe; and they are opposed, respectively, by three false principles: atheism, religious fatalism (which refers all moral distinctions to the will of God), and the fatalism of the ancient Stoics (who recognized God and yet identified him with nature).

Cudworth criticizes two main forms of materialistic atheism: the atomic (adopted by Democritus, Epicurus and Thomas Hobbes); and the hylozoic (attributed to Strato of Lampsacus, which explains everything by the supposition of an inward self-organizing life in matter).

Cudworth believes that atomism was first invented before the Trojan war by a Sidonian thinker named Moschus or Mochus (whom he identifies with Moses in the Old Testament).

This led many readers to accuse Cudworth himself of atheism – as John Dryden remarked, "he has raised such objections against the being of a God and Providence that many think he has not answered them".

[99] Much attention was also attached to a subordinate matter in the book, the conception of the "Plastic Medium" (a revival of Plato's "World-Soul") which was intended to explain the existence and laws of nature without referring to the direct operation of God.

This theory occasioned a long-drawn controversy between Pierre Bayle and Georges-Louis Leclerc, with the former maintaining, and the latter denying, that the Plastic Medium is favourable to atheism.

Summing up the work, Andrew Dickson White wrote in 1896: To this day he [Cudworth] remains, in breadth of scholarship, in strength of thought, in tolerance, and in honesty, one of the greatest glories of the English Church ...