Immunohistochemical techniques (IHC) and in situ hybridization (ISH) are widely used techniques to study the expression of proteins and messenger RNAs in tissues and are extremely important to confirm and interpret biochemical and molecular results from the same tissues. Investigation of human brain by IHC and ISH therefore still plays an important role in the elucidation of pathogenetic mechanisms in diseases such as multiple sclerosis. In this review we describe the processing of human brain tissues as well as basic and advanced immunohistochemical staining and ISH techniques used for neuropathological analysis of such pathological brains.