The present invention provides methods for treating subjects having or at risk of having a neuropathological disorder or brain inflammatory diseases with and without vascular involvement, and systemic inflammatory vascular disease by administering a therapeutically effective amount of Activated Protein C (APC) to the subject. Brain disorders and brain inflammatory vascular diseases that can be treated by the invention method include all neurodegenerative diseases with different types of neuronal dysfunction, including stroke, Alzheimer's disease, Parkinson's disease, Huntington disease, neuroimmunological disorders such as multiple scelrosis and Gullian-Barre, encephalitis, meningitis, as well as other peripheral vascular diseases, such as diabetes, hypertension, artheriosclerosis. Also included are methods of treatment using APC in combination with a co-factor, such as Protein S.