- First Letter Concerning Toleration (1689)
- Two Treatises of Government (1689)
- An Essay Concerning Humane Understanding (1689)
- Second Letter Concerning Toleration (1690)
- Third Letter Concerning Toleration (1692)
- Some Thoughts Concerning Education (1693)
- The Reasonableness of Christianity (1695)
- A Vindication of The Reasonableness of Christianity from Mr. Edwards's Reflections (1695)
- A Second Vindication of The Reasonableness of Christianity (1697)