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Publications on classical Arabic literature the Greek heritage in Arabic Islamic civilization and on the history of Islam; among others:
Die arabischen Übersetzungen von Aristoteles’ Schrift De Caelo (Frankfurt a/M 1966)
Proclus Arabus: Zwanzig Abschnitte aus der Institutio Theologica in arabischer Übersetzung. eingeleitet, herausgegeben und erklärt, Beiruter Texte und Studien, 10 (Beirut, Wiesbaden 1973)
The works of Yaḥyā ibn ʿAdī: an analytical inventory (Wiesbaden, 1977)
A Greek and Arabic Lexicon: materials for a dictionary of the mediaeval translations from Greek into Arabic (with Dimitri Gutas, Leiden 1992ff.)
Ed., Averroes and the Aristotelian Tradition (Leiden 1999)
Islam, an historical introduction, 2nd ed., Edinburgh 2002
‘Alexander of Aphrodisias on the First Cause: Aristotle’s First Mover in an Arabic treatise attributed to Alexander of Aphrodisias,’ in: Aristotele e Alessandro di Afrodisia nella tradizione araba, ed. da C. D’Ancona e G. Serra, Padova 2001, 19–74
‘Mathematics and philosophy in medieval Islam’, in: The Enterprise of Science in Islam: new Perspectives, ed. by Jan P. Hogendijk and Abdelhamid I. Sabra (Cambridge, Mass., 2003), 121–76;
Der arabische Aristoteles und sein Leser: Physik und Theologie im Weltbild Alberts des Großen (Paderborn 2004)
‘Die dreifache Ancilla: Hermeneutik und Logik im Werk des Sayf-al-Dīn al-Āmidī (1156–1233),’ in Logik und Theologie: das Organon im arabischen und im lateinischen Mittelalter, ed. D. Perler, U. Rudolph (Leiden 2005), 117-45
Der Islam in Daten (München 2006)
‘Building the library of Arabic philosophy: Platonism and Aristotelianism in the sources of al-Kindī,’ in: The Libraries of the Neoplatonists, ed. by C. D’Ancona (Leiden [etc.] 2007, 319–50.
For a full list of publications up to 2005 see: Rüdiger Arnzen and Jörn Thielmann, eds., Words, Texts and Concepts Cruising the Mediterranean Sea: Studies on the Sources, Contents and Influences of Islamic Civilization and Arabic Philosophy and Science Dedicated to Gerhard Endress on His Sixty-Fifth Birthday, Orientalia Lovanensia Analecta, 139 (Leuven: Peeters, 2004).
Co-editor of the journal Oriens (Leiden: Brill, since 1994).
Long-term research projects funded by the German Research Foundation (Deutsche Forschungsgemeinschaft):
Glossarium Graeco-Arabicum, an historical reference lexicon of the mediæval Arabic translations from the Greek, especially of scientific, medical and philosophical texts.  Since 2010, funded by the European Research Council project Greek into Arabic.
Averrois Opera, a critical edition of the works of Abū l-Walīd Ibn Rušd (Averroes), notably his commentaries on the works of Aristotle. 
Bioethical Issues in the Context of Islamic Law and its Interpretation by Members of the Medical Professions, funded by the DFG 2003–2004 as part of an interdisciplinary research group “Cross-cultural Bioethics. Conditions, Prospects, and Challenges”, 2005–2009 as a project of the Seminar für Orientalistik und Islamwissenschaften, University of Bochum.