In vivo microdialysis sampling extracellular excitatory and inhibitory amino acids from the striate cortex of mammals will provide important information for visual system research. To facilitate the interpretation of microdialysis results, this protocol critically examines: (1) the location of probe implantation in the visual cortex using Nissl staining; (2) the morphological changes after probe implantation by visualization of neurons containing glutamate; (3) the morphological changes after probe implantation by visualization of gliosis using glial fibrillary acidic protein (GFAP) immunocytochemistry; (4) the implantation of the probe in sensory-deprived versus non-deprived cortical regions by visualization of neurons containing c-Fos protein after limited retinal lesion. The histochemical and immunocytochemical methods of Glu, GFAP and c-Fos used are described.