Glioblastoma multiforme (GBM) is an almost uniformly fatal brain tumor; patients have a median survival time of less than one year despite aggressive treatments, including surgery, radiation and chemotherapy. Despite the clear benefits of radiation therapy in prolonging the survival of some patients with GBM, only about one-third of them demonstrate an objective radiographic response. To pinpoint the genetic difference between GBMs that responded well to radiation treatment and those that did not, we analyzed the gene expression profiles of two nonresponding (NR) and two responding (R) tumors using Affymetrix Hu6800 oligonucleotide arrays. Comparison between two paired tumor samples (R versus NR) revealed that 423 and 236 genes were differentially expressed (sort score 0.5). Of those, 33 genes showed consistently increased or decreased expression in both R tumors compared with NR tumors. These differentially expressed genes are known to regulate cell motility, cellular responses to DNA damage, cell cycle, angiogenesis and apoptosis. For example, decreased expression of genes known to stimulate tumor cell motility and increased expression of genes that inhibit cell migration was observed in R tumors. We also determined the gene expression of six candidate genes by real-time polymerase chain reaction quantitation analysis of four GBM samples. Investigation of these genes should help provide important insights into the biological mechanisms at work, facilitate identification of tumors that are susceptible or resistant to radiation therapy and aid in the design of approaches to enhance specifically the radiosensitivity of these deadly neoplasms.