The primary focus of this article is to examine the concept of cultural affiliation from the perspective of biological anthropology. The concept of cultural affiliation is fundamental to federal repatriation legislation including the Native American Graves and Repatriation Act (NAGPRA). Biological anthropologists are frequently called upon to assist museums and federal agencies with making determinations of cultural affiliation of human remains and associated funerary objects and objects of cultural patrimony as required by NAGPRA. Here, we present a case study from the American Southwest as a vehicle to more closely examine the role biological anthropologists play in the implementation of NAGPRA, and how the law has created tension or conflict within the field. We also examine more closely the concept of cultural affiliation as it pertains specifically to the law's regulations detailing its implementation. As a case study, we examine the process and history leading to the publication of the Notice of Inventory Completion for the human remains and funerary objects from Chaco Culture National Historical Park. Our case study includes an administrative history and a review of the biological evidence presented in the literature. The larger implications of our case study are that in addition to varying interpretations of NAGPRA, there are indications that biological anthropology is still struggling to overcome its typological perspective on biological variation. This perspective limits the field's ability to study cultural identity – past and present.