Quantum chromodynamics (QCD), the microscopic theory of strong interactions, has not yet been applied to the calculation of nuclear wavefunctions. However, it certainly provokes a number of specific questions and suggests the existence of novel phenomena in nuclear physics which are not part of the traditional framework of the meson-nucleon description of nuclei. Many of these phenomena are related to high nuclear densities and the role of colour in nucleonic interactions. Quantum fluctuations in the spatial separation between nucleons may lead to local high-density configurations of cold nuclear matter in nuclei, up to four times larger than typical nuclear densities. We argue here that experiments utilizing the higher energies available upon completion of the Jefferson Laboratory energy upgrade will be able to probe the quarkgluon structure of such high-density configurations and therefore elucidate the fundamental nature of nuclear matter. We review three key experimental programmes: quasi-elastic electro-disintegration of light nuclei, deep inelastic scattering from nuclei at x > 1 and the measurement of tagged structure functions. These interrelated programmes are all aimed at the exploration of the quark structure of high-density nuclear configurations.The study of the QCD dynamics of elementary hard processes is another important research direction and nuclei provide a unique avenue to explore these dynamics. In particular, we argue that the use of nuclear targets and large values of momentum transfer at energies available with the Jefferson Laboratory upgrade would allow us to determine whether the physics of the