Naturally enough, the interrelations between medieval Christian dualist doctrinal traditions, on the one hand, and medieval redactions of early Jewish and Christian pseudepigraphic literature on the other, were not among the main subjects of early scholarly study of medieval European dissent and heresy. But in the nineteenth and twentieth centuries that study was revolutionized by the publication of major primary sources for the history and doctrines of medieval Eastern and Western Christian dualism, which triggered substantial revisions of the assumptions and theses of early modern Protestant and Catholic polemical heresiology. However, the early scholarly exploration and, to some extent, even the modern study of medieval dualist heresy remain affected by the legacy of Catholic–Protestant polemical controversies that began as early as the sixteenth century, concerning the nature and teachings of medieval heretical, dissenting and reformist groups.

In these disputes Protestant scholars frequently understood the Cathars as dissenters reviving the spirit of early Christian communities in the face of the corruption and oppressions of the medieval Church; such scholars saw the Cathars as antecedents of the Waldensians (and hence forerunners of the Reformation), and routinely treated the accounts of their dualist and docetic doctrines as deliberate polemical misrepresentations by their Catholic adversaries. Medieval Catholic polemics and heresiology had habitually located the origins of the Cathars among medieval eastern dualist sectarians: these were considered the offspring of the ancient Manichaean heresy, and held to be the vehicle by which that heresy was transmitted to the western heretical communities identified as ‘Cathar’. Accordingly, early Protestant scholarship was liable to minimize and de-emphasize the existence, nature or provenance of dualist (routinely defined as ‘Manichaean’) teachings among the eastern dualist groups, due to their assumed and posited genealogical link (via the Cathars and Waldensians) to the later reformed Churches. Post-Reformation Catholic heresiological authorities like Benoist or Bossuet could reconstruct similar genealogies linking the eastern dualist communities to the Cathars and then to the Huguenots, but in their case with the goal of the exploiting these postulated heretical dualist connections to dent the theological and political credibility of their Protestant opponents.