Hamilakis has published papers on a wide variety of topics in archaeology and beyond. His most recent work involves the excavation of a Middle Neolithictell site in central Greece, where he also hosts a range of art projects, including a theatre-archaeology program. He is a prominent advocate of combining ethnography, art, and community engagement in archaeological fieldwork, in the interest of "a politically committed archaeological and academic practice, devoted to social justice."[6] He has also written on the politics of pedagogy and his attempts to create a "border pedagogy" in his teaching.
The Nation and its Ruins: Archaeology, Antiquity and National Imagination in Modern Greece, Oxford University Press, 2007. ISBN9780199230389.
Archaeologies and the Senses: Human Experience, Memory, and Affect, Cambridge University Press, 2013. ISBN9780521837286.
Hamilakis, Y. and Ifantidis, F. 2016. Camera Kalaureia: An Archaeological Photo-ethnography | Μια Αρχαιολογική Φωτο-Εθνογραφία Oxford: Archaeopress.
Χαμηλάκης, Γ. 2012. Το Έθνος και τα Ερείπιά του. Αρχαιότητα, Αρχαιολογια, και Εθνικό Φαντασιακό στην Ελλάδα. Αθήνα: Εκδόσεις του Εικοστού Πρώτου (translated by Nektarios Kalantzis).
Χαμηλάκης, Γ. 2015. Η Αρχαιολογία και οι Αισθήσεις. Βίωμα, Μνήμη, και Συν-κίνηση. Αθήνα: Εκδόσεις του Εικοστού Πρώτου (translated by Nikos Kourkoulos).
Greenberg, R. and Hamilakis, Y. 2022. Archaeology, Nation, and Race: Confronting the Past, Decolonizing the Future in Greece and Israel. Cambridge: Cambridge University Press.[11]
As editor:
Rainbird, P. and Hamilakis, Y. (eds) 2001 Interrogating Pedagogies: Archaeology in Higher Education. Oxford: BAR/Archaeopress. Pp. 120 (ISBN1-84171-240-X).
The Usable Past: Greek Metahistories, Lexington Books, 2003. ISBN0-7391-0384-9.
Thinking Through the Body: Archaeologies of Corporeality, Kluwer/Plenum, 2002. ISBN0306466481.
Kotjabopoulou, E., Hamilakis, Halstead, P., Gamble, C., and Elefanti, V. (eds). 2003. Zooarchaeology in Greece: Recent Advances. London: BSA. (ISBN0904887413).
Hamilakis, Y. and Duke, P. (eds) 2007. Archaeology and Capitalism: From Ethics to Politics. Walnut Creek, CA: Left Coast Press.
Hamilakis, Y. and Labanyi, J. (eds) 2008. Remembering and Forgetting in Europe’s Southern Periphery. Special Issue of the journal, History and Memory (vol. 20, issue 2).
Carabott, P., Hamilakis, Y. and E. Papargyriou, E. (eds) 2015. Camera Graeca: Photographs, Narratives, Materialities. London: Ashgate.
Hamilakis, Y. and Jones A. (eds) 2017 Archaeology and Assemblage (special thematic issue of the Cambridge Archaeological Journal vol. 27(1).
Hamilakis, Y. (ed.). 2017 [2016] Archaeologies of Forced and Undocumented Migration (Special, thematic issue of the Journal of Contemporary Archaeology, 3(2).
Hamilakis, Y. and Momigliano, N. (eds) 2010. Αρχαιολογία και Ευρωπαϊκή Νεοτερικότητα. Παράγοντας και Καταναλώνοντας τους “Μινωίτες”. Αθήνα. Εκδόσεις του Εικοστού Πρώτου (μτ. Νίκος Κούτρας).
^Hamilakis, Yannis (2014). Archaeology and the senses : human experience, memory, and affect. Cambridge: Cambridge University Press. p. iv. ISBN9780521837286.