In 2004, having received the John W. Kluge Prize for Lifetime Achievement in the Human Sciences, Pelikan donated his award to Saint Vladimir's Orthodox Theological Seminary, of which he is a trustee.
On May 13, 2006, Jaroslav Pelikan reposed, after a long battle with lung cancer. The funeral was May 17 in the seminary chapel of St. Vladimir's Seminary.
- What is the difference between Tradition and Traditionalism? Tradition is the living faith of the dead. Traditionalism is the dead faith of the living.
- For those who believe that you don't need tradition because you have the Bible, the Christian Tradition has sought to say, "You are not entitled to the beliefs you cherish about such things as the Holy Trinity without a sense of what you owe to those who worked this out for you." To circumvent Saint Athanasius on the assumption that if you put me alone in a room with the New Testament, I will come up with the doctrine of the Trinity, is naive. So for these readers I have tried to provide a degree of historical sophistication, which is, I believe, compatible with an affirmation of the central doctrines of Christian faith.
- Bach Among the Theologians
- Christianity and Classical Culture: The Metamorphosis of Natural Theology in the Christian Encounter with Hellenism, Yale University, 1995, ISBN 0300062559
- Confessor Between East and West: A Portrait of Ukrainian Cardinal Josyf Slipyj
- Credo: Historical and Theological Guide to Creeds and Confessions of Faith in the Christian Tradition ISBN 0300093888
- Development of Christian Doctrine: Some Historical Prolegomena
- The Excellent Empire: The Fall of Rome and the Triumph of the Church
- Faust the Theologian
- The Idea of the University: A Reexamination ISBN 0300058349
- Interpreting the Bible and the Constitution (John W. Kluge Center Books) ISBN 0300102674
- Jesus Through the Centuries: His Place in the History of Culture ISBN 0300079877
- Luther's Works
- Martin Luther's Basic Theological Writings
- Mary Through the Centuries: Her Place in the History of Culture ISBN 0300076614
- Mary: Images Of The Mother Of Jesus In Jewish And Christian Perspective
- The Melody of Theology: A Philosophical Dictionary
- The Reformation of the Sixteenth Century (Foreword) ISBN 0807013013
- The Riddle of Roman Catholicism
- The World Treasury of Modern Religious Thought
- What Has Athens to Do with Jerusalem?: Timaeus and Genesis in Counterpoint (Thomas Spencer Jerome Lectures) ISBN 0472108077
- Whose Bible Is It? A History of the Scriptures Through the Ages ISBN 0670033855
- Jaroslav Pelikan article in German
- Yale History Faculty: Jaroslav Pelikan
- Pelikan to Orthodox church by Roger Kahle and Amy Sitze of thelutheran.org (subscription only)
- Announcement of Kluge Award
- "The Future of Our Past" - originally published in The Orthodox Church (OCA newspaper)
- The Predicament of the Christian Historian by Jaroslav Pelikan