- The True Story of John Smyth, the Se-Baptist: As Told by Himself and His Contemporaries; With an Inquiry Whether Dipping Were a New Mode of Baptism in England, in or about 1641 (Classic Reprint)
- Street Thoughts
- What Ought to Be Done with the Freedmen and with the Rebels? a Sermon Preached in the Berkeley-Street Church, Boston, on Sunday, April 23, 1865
- The Congregationalism of the Last Three Hundred Years, as Seen in Its Literature: With Special Reference to Certain Recondite, Neglected, or Disputed Passages, Volume 4
- The Congregational Quarterly, Volume 5