Cell-based therapy has been widely evaluated in spinal cord injury (SCI) animal models and shown to improve functional recovery. However, host response to cell transplants at gene expression level is rarely discussed. We reported previously that acute transplantation of radial glial cells RG3.6 following SCI promoted early locomotion improvement within 1 week post-injury. To identify rapid molecular changes induced by RG3.6 transplantation in the host tissue, distal spinal cord segments were subjected to microarray analysis. Although RG3.6 transplantation, reduced activity of macrophages as early as 1-2 weeks post-injury, the expression levels of inflammatory genes (e.g., IL-6, MIP-2, MCP-1) were not decreased by RG3.6 treatment as compared to medium or other cell controls at 6-12 h post-injury. However, genes associated with tissue protection (Hsp70 and Hsp32) and neural cell development (Foxg1, Top2a, Sox11, Nkx2.2, Vimentin) were found to be significantly up-regulated by RG3.6 transplants. Foxg1 was the most highly induced gene in the RG3.6-treated spinal cords, and its expression by immunocytochemistry was confirmed in the host tissue. Moreover, RG3.6 treatment boosted the number of Nkx2.2 cells in the spinal cord, and these cells frequently co-expressed NG2, which marks progenitor cells. Taken together, these results demonstrate that radial glial transplants induced rapid and specific gene expression in the injured host tissue, and suggest that these early responses are associated with mechanisms of tissue protection and activation of endogenous neural progenitor cells.