Shaffer is noted for his studies on the Indus Valley Civilization. According to him there is no archaeological indication of an Aryan migration into northwestern India during or after the decline of the Harappan city culture.
Jim G. Shaffer (1984). "The Indo-Aryan Invasions: Cultural Myth and Archaeological Reality". In John R Lukacs. The People of South Asia: The Biological Anthropology of India, Pakistan and Nepal. New York: Plenum Press. pp. 77–88.
Prehistoric Baluchistan: With Excavation Report on Said Qala Tepe.
A Honaki Phase Site on the Lower Verde River, Arizona.
Jim G. Schaffer (1995). ""Cultural tradition and Palaeoethnicity in South Asian Archaeology"". In Ed. George Erdosy. Indo-Aryans of Ancient South Asia. ISBN3-11-014447-6.
Jim G. Schaffer (1999). "Migration, Philology and South Asian Archaeology". In Bronkhorst; Deshpande. Aryan and Non-Aryan in South Asia. ISBN1-888789-04-2.
Jim G. Schaffer (1993). "Reurbanization: The Eastern Punjab and Beyond". In H. Spodek; D.M. Srinivasan. Urban Form and Meaning in South Asia: The Shaping of Cities from Prehistoric to Precolonial Times. Studies in the History of Art No. 31. Washington DC: National Gallery of Art. pp. 53–67.
Jim G. Shaffer (1992). "The Indus Valley, Baluchistan and Helmand Traditions: Neolithic Through Bronze Age". In R. W. Ehrich. Chronologies in Old World Archaeology (Second ed.). Chicago: University of Chicago Press. pp. I:441-464, II:425-446.
^Shaffer, J. and D. Lichtenstein, 1999. “Migration, Philology and South Asian Archaeology.” In Aryan and Non-Aryan in South Asia: Evidence, Interpretation and Ideology, edited by J. Bronkhorst and M. Deshpande. Cambridge, MA: Harvard University Press.