Using the suppression subtractive hybridization (SSH) strategy for differential gene cloning, we identified the induced expression of a rat homologue to murine and human monocyte chemotactic protein-3 (MCP-3) in ischemic brain. The 2.4-kilobase rat MCP-3 gene features high homology in gene structure and sequence to murine MCP-3. The temporal expression of MCP-3 mRNA was examined in brain tissue rendered ischemia by permanent or temporary occlusion of the middle cerebral artery (MCAO). A marked increase in MCP-3 mRNA was observed 12 h post-ischemia, with 49-fold and 17-fold increase (n=4, p<0.01) over control in the permanent or temporary MCAO, respectively. Significant induction of MCP-3 in the ischemic cortex was sustained up to 5 days after ischemic injury. The profile of MCP-3 mRNA induction paralleled leukocyte infiltration and accumulation that occur after focal stroke, suggesting a role for MCP-3 in recruiting these inflammatory cells into the ischemic tissue. Molecular cloning of rat MCP-3 should provide a valuable tool, as demonstrated in the present work, for the investigation of MCP-3 expression and function in rat disease models.