1630 – God’s Promise to His Plantation. as It Was Delivered in a Sermon by John Cotton, B.D. and Preacher of Gods Word in Boston., London: Printed by William Jones for John Bellamy, and are to be solde at the three Golden Lyons by teh Royall Exchange, 1630.
1636 – A Sermon preached at Salem with a Retraction of his former Opinion concerning Baptism. Boston.
1641 – An Abstract of the Lawes of New England As they are now established. London: Printed for F. Coules, and W. Ley at Paules Chain.
1641 – The Way of Life Or Gods Way and Course in Bringing the Soule Into Keeping it In and Carrying it On in the Wayes of Life and Peace Laid Downe in Foure Severall Treatises on Foure Texts. London: Printed by M.F for L. Fawne and S. Cellibrand at the Brasen Serpent in Pauls Church-yard.
1641 – The powring ovt of the seven vials or, An exposition, of the 16. chapter of the Revelation, with an application of it to our times. London: Printed for R.S. to be sold at Henry Overtons shop in popes-0head Alley.
1642 – A Brief Exposition of the Whole Book of Canticles, or Song of Solomon, London: Printed for Philip Nevil at the sign of the Gun in Ivie-Lane.
1642 – The Chuches Resurrection, or The Opening of the Fifth and Sixth Versus of the 20th Chapter of the Revelation, London: Printed for Henry Overton to be sold at his shop in Popes-head Alley.
1642 – The True Constitution of a Particular Visible Church, Proved by Scripture. London: Published by Samuel Satterthwaite at the signe of the Black bull in Budge rowe, neare to Saint Antholines church.
1642 – A Modest and Cleare Answer to Mr. Ball’s Discourse of Set Formes of Prayer. London
1644 – The Keyes of the Kingdom of Heaven: and Power thereof, according to the Word of God. London: Printed by M. Simmons for Henry Overton to be sold at his shop entering into Popes-head Alley.
1644 – Sixteene questions of seriovs and necessary consequence, propounded unto Mr. John Cotton of Boston in New England together with his answer to each question. London: Printed by E.P. for Edward Blackmore.
1646 – Milk for Babes. Drawn Out of the Breasts of Both Testaments. Chiefly, for the Spirituall Nourishment of Boston Babes in eithr England: But may be of like use for any Children. London: Printed by J. Coe for Henry Overton to be sold at his Shop in Popes-head Alley.
1647 – The Bloudy Tenent, Washed and Made White in the Bloud of the Lambe. London: printed by Matthew Symms for Hannah Allen at the Crowne in Popes Head-Alley
1647 – A Reply to Mr. Williams his Examination, and Answer of Letters sent to him. London
1647 –The Grounds and Ends of Baptisme of the Children of the Faithfull. Epistle by Th. Goodwine. London.
1647– Singing of Psalmes a Gospel Ordinance. London
1648 – The Way of Congregational Churches Cleared. In Two Treatises. London
1648 – Thomas Hooker. Survey of the Summe of Church Discipline. London
1650 – Of the Holinesse of Church Members. London
1651 – Christ the Fountaine of Life: or, Sundry Choyce Sermons on Part of the Fift Chapter of the First Epistle of St. John. London: Printed by Robert Irbitson.
1654 – A Briefe Exposition with Practicall Observations Upon the Whole Book of Ecclesiastes. London: published by Anthony Tuckney, D.D., Master of St. Johns Colledge in Cambridge and printed by T.C. for Ralph Smith at the Bible in Cornhill.
1655 – An Abstract of Laws and Government. Published by William Aspinwall. London
1656 – A Practicall Commentary, or an Exposition with Observations, Reasons, and Uses Upon the First Epistle Generall of John, London: Printed by R.I. and E.C. for Thomas Parkhurst to be sold at the Three Crownnes at the lower end of Cheapside.
1659 – A Treatise of the Covenant of Grace, as It Is Dispensed to the Elect Seed, Effectuall Unto Salvation. London.
1660 – Some Treasure Fetched out of Rubbish, Or Three short but seasonable Treatises (found in a heap of featured Papers), which Providence has reserved for their Service who desire to be instructed, from the Word of God, concerning the Imposition and Use of Significant Ceremonies in the Worship of God. London.
1663 – A Discourse about Civil Government in a New Plantation, whose Design is Religon. Cambridge.