1. Inštitut of Church History
Head: Full Professor Bogdan Kolar, Ph.D.
2. Institute of Philosophy and Social Ethics
Head: Associate Professor Bojan Žalec, Ph.D.
3. Institut of Bible, Judaism and Early Christianity
Head: Associate Professor Maria Carmela Palmisano, Ph.D.
4. Institute of Moral Theology and Spiritual Questions of Modern Culture
Head: Associate Professor Ivan Štuhec, Ph.D.
5. Institute of Patristic Studies
Head: Assistant Professor Miran Špelič, Ph.D.
6. Institute of Canon Law
Head: Associate Professor Stanislav Slatinek, Ph.D.
7. Institute of Psychology and Sociology of Religion and of Marital and Family Therapy
Head: Assistant Professor Igor Bahovec, Ph.D.
8. Institute of Applied Theology
Head: Assistant Professor Andrej Šegula, Ph.D.
9. Stanko Janežič Institute of Dogmatic, Fundamental and Ecumenical Theology and of Religiology and Dialogue
Head: Assistant Professor Mari Jože Osredkar, Ph.D.
10. Institute of Bioethics
Head: Full Professor Robert Petkovšek, Ph.D.