The design and application of bionanotechnologies aimed at the central nervous system (CNS) provide powerful new approaches for studying cell and molecular biology and physiology. Emerging clinically oriented bionanotechnologies are targeting CNS pathologies such as trauma or degenerative events. The successful and meaningful development of bionanotechnologies designed to interact with the CNS as research or clinical tools require an understanding of the relevant neurophysiology and neuropathology, an appreciation of the inherent nanoscale structure of the CNS, and an understanding of the relevant chemistry and materials science and engineering. This review gives an introduction to the structure and organization of the CNS starting at the organ level and working down in spatial scale to the cellular and molecular levels, with specific examples of biological nanoengineering in neural cells. This is followed by a discussion of some of the unique challenges and obstacles associated with developing bionanotechnologies aimed at the CNS, and a discussion of emerging nanotechnologies for neuroscience applications.