Neuropathological techniques such as conventional and immunohistochemical staining of paraffin-embedded tissue sections are instrumental for identification and characterization of aberrations of organ architecture during human inflammatory disorders of the central nervous system (CNS) as in their animal models. Here we describe step-by-step protocols for tissue processing, sectioning, and conventional and immunohistochemical stainings to display as well as quantify CNS inflammation, demyelination, and neuronal damage in experimental autoimmune encephalomyelitis (EAE), an animal model of Multiple Sclerosis (MS).