THE heterogeneity of c-fos and hsp72 mRNA expression during focal ischemia was studied in mice by combiningin situhybridization with metabolic imaging. Focal ischemia was produced by middle cerebral artery occlusion for 3 h. The infarct core and the penumbra were differentiated by regional ATP and cerebral protein synthesis (CPS) imaging. hsp72 mRNA expression was restricted to the ischemic penumbra, as defined by the dissociation between preserved ATP and suppressed CPS. c-fos mRNA was expressed not only in the penumbra but also in the peri-ischemic normal brain tissue in which both ATP and CPS were preserved. These data demonstrate a highly selective differential expression of immediate-early and stress-related genes in the peri-infarct surrounding which is explained by different mechanisms of gene induction.