Emerging from the philological-historical approaches of the eighteenth-century Orientalists, the scientific study of the hominid fossil record and prehistory of South Asia (India, Pakistan, Sri Lanka, and their borderlands) has a history of over two centuries. Today Western and South Asian scholars offer new answers to old questions about the origin and antiquity of the earliest hominids in the subcontinent, the beginnings of the Indus civilization, archaeological and skeletal interpretations about the reputed Indo-European-speaking Aryans of the Vedic tradition, biological affinities of ancient and modern populations, and palaeodemographic profiles of health and disease status, traumatic and developmental modifications, and population sizes and densities of earlier peoples in this part of Asia. At the beginning of the third millennium we respond to these issues in ways that modify or repudiate earlier theories and interpretations of archaeological and palaeontological data, e.g., a present-day recognition that hominids were present in the northwestern sector of the subcontinent during the geological period of the Pliocene-Pleistocene transition, the establishment of the roots of the Indus civilization in cultures established by 7000 B.C. and long before the period of the third millennium B.C. settlement and cultural diffusion, the fall of the Aryan migration myth and its racial and caste implications, and a reevaluation of population genetic affinities using DNA and more powerful statistical types of analysis of the skeletal record. This paper summarizes these and other recent advances in South Asian palaeoanthropology by noting transitions in scientific perspectives and present-day issues of research, and discusses prospects for the development of palaeoanthropology in South Asia at the dawn of the new millennium in the light of specific crises that will be encountered by its future practitioners.