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Microscopical examination of brain tissue appears as a valuable process, which can acknowledge, complete or confute the acquired findings by functional experiments. The purpose of this work was to survey histo-morphological and functio-morphological techniques mostly used in the neuropathophysiological research with application examples. The most common pathological processes in the brain is possible to document with some of this methods. Whether there are developmental, traumatical, degenerative, on the base of ischemia, reperfusion developed or only functional changes. The work deals with methods histological-non-specific, that offer comprehensive image- as hematoxiline-eosine staining, Nissl staining, Golgi impregnation. Further with cyto- and histochemical techniques- as Fluoro-Jade staining and NADPH-diaphorase detection and with immunohistochemical methods, in which marking with anticalbindin and imaging of c-fos protein are noted.