Museum Østjylland har sin egen videnskabelige bogserie, Museum Østjyllands Publikationer (East Jutland Museum Publications), som udgives af Aarhus Universitetsforlag. I serien publiceres forskning i Museum Østjyllands ansvarsområde udført af museets eget personale eller af eksterne forskere.
Bind 1. E. Stidsing/K. Høilund Nielsen/R. Fiedel (eds.). Wealth and Complexity. Economically specialised sites in Late Iron Age Denmark. East Jutland Museum Publications vol. 1 (Århus 2014).
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Bind 2. Lutz Klassen, Along The Road. Aspects of Causewayed Enclosures in South Scandinavia and Beyond. East Jutland Museum Publications vol. 2 (Århus 2014).
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Bind 3. Inger Marie Hyldgaard, Tjærby Ødekirke og Ødekirkegård. Museum Østjyllands Publikationer vol. 3 (Århus 2016).
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Bind 4. Søren H. Andersen, Vængesø and Holmegaard. Ertebølle Fishers and Hunters on Djursland. East Jutland Museum Publications vol. 4 (Århus 2018).
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Bind 5. Lutz Klassen (ed.), The Pitted Ware Culture on Djursland. Supra-regional significance and contacts in the Middle Neolithic of southern Scandinavia. East Jutland Museum Publications vol. 5 (Århus 2020).