Identification of genes mediating glioma invasion promotes the understanding of glia motility and might result in biologically based therapeutic approaches. Most experimental studies have been performed in vitro, although glial cells typically undergo marked phenotypic change following placement into cell culture. To evaluate migration mechanisms operating in vitro versus in vivo, we used C6 rat glioblastoma cells for selecting highly migratory cells in a monolayer migration assay as well as in brains of nude mice, and analyzed in each paradigm the expression profiles of these "fast" cells versus those of the original "slow" cells using oligonucleotide microarrays comprising 8832 genes. In vitro, 516 (10.6%) of 4848 expressed genes were regulated (i.e., differentially expressed in fast versus slow cells); 916 genes were expressed only in vitro, including 142 (15.5%) regulated genes. In vivo, 245 (6.1%) of 4044 expressed genes were regulated; 112 genes were expressed only in vivo, including 25 (22.3%) regulated genes, none of them having a known relation to glioma invasion. Of 730 regulated genes, only 31 (4.2%) were regulated in parallel in vitro and in vivo, most of them having a known relation to (glioma) invasion. Our data provide new molecular entry points for identifying glioma invasion genes operating exclusively in the brain. They further suggest that genes underlying glia cell motility are strikingly different in vitro and in vivo.