Molecular biological techniques have been used extensively to gain insights into the pathogenesis of a variety of diseases caused by neurotropic viruses. Increasingly sensitive methods for detecting viral nucleic acids and proteins in pathological nervous tissues have clarified the viral aetiology of certain neurological disorders and are now being used to investigate possible viral involvement in others. In addition, a diverse range of molecular techniques has greatly enhanced our understanding of the molecular basis of viral neurotropism and neurovirulence in both humans and experimental animals. This article provides an overview of these various approaches with examples drawn from both clinical neurological disease and animal models.