He is known for his historical theories and his investigations at Cahokia, the major center of precolonial Mississippian culture in the American Bottom region of Illinois near St. Louis, Missouri.
Early on, he met Brad Koldehoff, who was similarly exposed to archaeology while growing up on the other side of their home town of Millstadt, Illinois.
During college he worked as an intern for the U.S. Army Corps of Engineers, St. Louis District, learning from lead archaeologist Terry Norris, another veteran of the Mound 72 excavations at Cahokia.
A particularly memorable field encounter that he, Preston Miracle, and David Anderson had with the "dark forces" of American capitalism in 1987 is recorded in his 2007 book Chiefdoms and Other Archaeological Delusions.
[5] Pauketat has concentrated his own research on Cahokia, an Indigenous city at the center of a large, regional Mississippian culture that extended its influence up and down the Mississippi Valley and across its tributaries.
[7] The finding of similar mundane and ritual implements such as pottery, chunkey stones, and Mississippian stone statuary in locations as far afield as sites such as Spiro Mounds in Oklahoma, and the presence of resources from distant locales such as the Gulf of Mexico at Cahokia, show the extent of Cahokia's historical and political connections to the greater Mississippian world.
These villages have fewer finely crafted items or ritual objects and a high percentage of workshop debris, likely indicating their purpose as support communities for the Cahokian elite.
His notion of a transplanted farmer population is supported by the complete abandonment of these upland villages at the same time of Cahokia’s presumed collapse around two centuries later.
For instance, due to improvements in radiometric dating and new methodologies, such as identification of domestic remains, he and other researchers have concluded that Cahokia rose and fell over a much shorter time period, around three hundred years, than had been previously attributed.
While this distribution was most certainly due to an exchange network, Pauketat posits relations between Cahokians and other Mississippians as not being purely environmentally determined, following previous interpretations (by who?).
At a more local scale, the sudden appearance and proliferation of Cahokian artifacts is coupled with housing reorganization of peoples and the incorporation of greater Cahokia.
Though often much more limited in scope and time than academic archaeology, Pauketat's book, The Ascent of Chiefs..., details how artifacts in part “salvaged” from the construction of a highway through Cahokia can be used to achieve the highest kind of intellectual knowledge production.
Dividing up the artifacts by radiometrically dated and ceramic-seriated phases, he noted an increasing number of foreign goods as time progressed during the pre-Cahokian era.
[13] Traditions are the forms of practice most visible in the archaeological record; they can range from an arrowhead style to the preponderance of shell-tempered pottery throughout the U.S. Mid-South and Midwest during the Mississippian era.
Between 2009 and 2011, he worked with Danielle Benden and Robert Boszhardt (independent) to lead "The Mississippian Initiative" (funded by the National Science Foundation).
In Wisconsin, they found evidence that the effects of Cahokians colonizing the north country in the 11th century AD resulted in profound, long-term change in the precolonial Native world.
Between 2012 and 2018, Pauketat worked with Susan Alt (Indiana University, Bloomington) on an even larger-scale investigation of upland "shrine complexes" due east of Cahokia.
Over five intensive field seasons, Alt and Pauketat's teams undercovered evidence of periodic, large-scale religious events at a place dubbed the "Emerald Acropolis."
Here, Pauketat verified his claims that Cahokian religion was centered on the long 18.6-year cycle of the Moon, drawing inspiration from colleagues at Chaco Canyon, in New Mexico, and the Hopewell sites of central Ohio.
Since then, Alt and Pauketat have sought to understand the relationship between religion to politics generally, at sites in Wisconsin, Mississippi, Indiana, and Illinois.
Woods notes that James B. Griffin, "the dean of Eastern North American archaeology," repeatedly stated that there was "absolutely no evidence for direct contact between Mesoamerica and Cahokia.
"[15] C. Wesson says that Pauketat presents this theory but is not committed to proving a connection between Cahokia and ancient Mexico; rather it is one of several alternatives that he explores to provide an overview of the field.