BACKGROUND The toxicity of methanol is as a result of its metabolites, formaldehyde and formic acid. Formic acid induces severe metabolic acidosis causing death, and is the primary agent responsible for ocular toxicity. Glial fibrillary acidic protein (GFAP) immunostaining is the most commonly used method for examining astrocyte proliferation and hypertrophy after various central nervous system injuries. The antigen CD34 is expressed widely on vascular endothelium, including that of the central nervous system and high endothelial venules. METHODS In this study, GFAP and CD34 were immunohistochemically localised in the post-mortem optic nerve head, and brain tissue (basal ganglia putamen) samples were collected from methanol-exposed and non-methanol-exposed (control) subjects. RESULTS There was a positive correlation between the GFAP and CD34 intensity of staining scores in the methanol-exposed group (P=0.711, P=0.010). Furthermore, there was also a positive correlation between the brain putamen and optic nerve head GFAP extent of staining in the methanol-exposed group (P=0.720, P=0.008). A statistically significant difference was found between the methanol-exposed group and the control group optic nerve CD34 intensity scores (P=0.014), but no significant difference was found between optic nerve CD34 and GFAP extent scores (P=0.05). CONCLUSIONS The study revealed that methanol affects brain putamen and the optic nerve selectively. We detected a positive significant correlation between brain and optic nerve GFAP expression. CD34 expression was markedly decreased by the toxic effects of methanol.