Human gliomas occasionally show rearrangements with deletions (exons II to VII) in the epidermal growth factor receptor (EGFR) gene, resulting in the expression of aberrant EGFR mRNA. This abnormality of EGFR gene expression is closely related to the malignancy of glioma. However, this EGFR gene abnormality has not been demonstrated directly in the glioma cells themselves, as gliomas consist of heterogeneous tissue components. In this study, we used in situ hybridization (ISH) to detect aberrant EGFR mRNA in the tumor cells in 26 human gliomas and 19 human glioma xenografts. We used digoxigenin (DIG)-labeled antisense oligonucleotide probes for ISH, which demonstrated aberrant EGFR mRNA in 2 of the 26 gliomas and in 3 of the 19 human glioma xenografts. ISH with an aberrant EGFR-specific probe (oligo-PA) revealed that EGFR mRNA was absent from multinucleated giant cells and from proliferating endothelial cells, but this transcript was present in small glioma cells. Identical aberrant EGFR mRNA was confirmed in these glioma and human glioma xenografts by Southern blotting. Northern blotting, and by reverse transcription-polymerase chain reaction (RT-PCR). These findings suggest that small tumor cells specifically express the aberrant EGFR mRNA in certain high grade gliomas.