- The Dark Night of Resistance (1971)
- The Geography of Faith: Conversations Between Daniel Berrigan When Underground, and Robert Coles (1971)
- America is Hard to Find: Notes from the Underground and Letters from Danbury Prison (1972)
- Absurd Convictions, Modest Hopes: Conversations after Prison with Lee Lockwood (1972)
- Lights on in the House of the Dead (1974)
- Apostle of Peace: Essays in Honor of Daniel Berrigan edited by John Dear (1996)
- Daniel: Under the Siege of the Divine (1998)
- Uncommon Prayer: A Book of Psalms (1998)
- And the Risen Bread: Selected Poems, 1957 - 1997 (1998)
- The Bride: Images of the Church (2000)
- Lamentations: From New York to Kabul and Beyond (2003)
- Testimony: The Word Made Fresh (2004)
- Prayer for the Morning Headlines: On the Sanctity of Life and Death (2007)
- Daniel Berrigan: Essential Writings edited by John Dear (2009)