Cytoglobin, a new member of the mammalian heme-globin family has been shown to bind oxygen and to have cell protective properties in vitro. Cytoglobin is specifically expressed in a subpopulation of brain neurons. Based on hypoxia-induced up regulation and proposed scavenging of reactive oxygen species Cytoglobin was suggested as a candidate for pharmaceutical stroke treatment. Since production of reactive oxygen species is a hallmark of ischemia, we hypothesized that Cytoglobin expression would be increased and that Cytoglobin expressing neurons would be spared after ischemic injury. Twenty male C57BL/6J mice were used in the experimental design. Ten were sham operated and ten were given permanent middle cerebral artery occlusion (pMCAo). All animals were euthanized after 24h. From each group, three animals were used for histology and seven for QRT-PCR and western blotting. Immunohistochemical examination of the ischemic penumbra revealed neither changes in Cytoglobin immunoreactivity nor any changes in expression in the necrotic infarct area. The lack of expression change was confirmed by western blotting and QRT-PCR showing no significant difference between sham and pMCAo operated mice. This suggests that Cytoglobin is likely not important for global neuronal protection following ischemia and the role of Cytoglobin in relation to endogenous neuroprotection remains unresolved.