Precise localization of the causative disorder within the nervous system (neuroanatomical diagnosis) and an understanding of the suspected disease processes (differential diagnosis) are key to an accurate neurological diagnosis. The advantages of using sophisticated neurodiagnostic tests are undeniable, but unfortunately, despite the relatively high sensitivity, these tests lack specificity in identifying the exact nature of the disease process. This chapter deals with functional neuroanatomy and anatomical diagnosis, forebrain, brainstem, cerebellum, spinal cord, peripheral nerves, neuromuscular junction, muscle, differential diagnosis.