- Disarming the Heart: Toward a Vow of Nonviolence (1993)
- Apostle of Peace: Essays in Honor of Daniel Berrigan (1996)
- The Sound of Listening: A Retreat Journal from Thomas Merton's Hermitage (1999)
- Jesus the Rebel: Bearer of God's Peace and Justice (2000)
- Mohandas Gandhi: Essential Writings (2002)
- Mary of Nazareth, Prophet of Peace (2003)
- The Questions of Jesus: Challenging Ourselves to Discover Life's Great Answers (2004)
- Living Peace: A Spirituality of Contemplation and Action (2004)
- Peacework: Prayer, Resistance, Community (2005)
- You Will Be My Witnesses: Saints, Prophets, Martyrs (2006)
- Transfiguration: A Meditation on Transforming Ourselves and Our World (2007)
- A Persistent Peace: One Man's Struggle for a Nonviolent World (2008)
- Put Down Your Sword: Answering the Gospel Call to Creative Nonviolence (2008)
- Daniel Berrigan: Essential Writings edited by John Dear (2009)
- Lazarus, Come Forth!: How Jesus Confronts the Culture of Death and Invites Us into the New Life of Peace (2011)