Chemotherapy in itself is suspected to cause the development or selection of drug-resistant tumor cells, which have more aggressive phenotypes. The authors investigated the differential changes of gene expression in the 1-(4-amino-2-methyl-5-pyrimidinyl)-methyl-3-(2-chloroethyl)-3-nitrosourea (ACNU)-resistant subline of the C6 rat glioma (C6AR2), which was established from C6 rat glioma cells by exposure to ACNU in vitro. The resistance to ACNU of C6AR2 was confirmed by MTS assay. The increased expression of O(6)-methylguanine-DNA methyltransferase in C6AR2 cells was shown using RT-PCR. C6AR2 cells displayed a higher proliferative activity relative to C6 cells. Analysis with cDNA array showed that 19 genes were transcriptionally up-regulated and 16 genes down-regulated in C6AR2 cells compared to C6 cells. They belonged to various functional classes of genes beside the drug-resistant system. Among them, the down-regulation of several genes in C6AR2 cells, including c-kit, pleiotrophin, platelet-derived growth factor receptor-alpha, peripheral myelin protein-22 and NG2 chondroitin sulfate proteoglycan, which are expressed originally in developmental glial linages, were verified using semi-quantitative RT-PCR. In addition, the gene expression of astroglial intermediate filament proteins, including GFAP, vimentin and nestin, were decreased in C6AR2 cells relative to C6 cells in semi-quantitative RT-PCR and immunocytochemistry. These findings may represent an undifferentiated state of ACNU-resistant glioma cells and a more aggressive phenotype in recurrent tumors following chemotherapy.