The peripheral primitive neuroectodermal tumors (pPNETs) of childhood, including Ewing's sarcoma, peripheral neuroepithelioma, and Askin's tumor, often present significant diagnostic challenges for the anatomic pathologist. One consistent feature of these tumors is the presence of the t(11;22)(q24;q12) in tumor cells, and this translocation has been useful as a marker for this group of tumors. The recent cloning of the t(11;22) breakpoint has revealed the fusion of the human FLI-1 gene on chromosome 11q24 with a gene of unknown function called EWS on 22q12, and fusion transcripts have been detected. These findings have raised the possibility of using molecular genetic analysis as a tool to diagnose pPNETs. To this end, we have tested pPNETs for the presence of EWS/FLI-1 fusion transcripts by reverse transcriptase-polymerase chain reaction (RT-PCR) using EWS and FLI-1 specific primers. Eight (80%) of 10 pPNET cell lines were positive for amplified products using this technique. These results were confirmed by Southern analysis, which revealed rearrangements of EWS using genomic EWS probes in all eight positive cell lines. We then tested 20 primary pPNET tumors, and identified fusion transcripts by RT-PCR in 18 (90%) of these cases. Cloning and sequencing of PCR products confirmed the presence of EWS and FLI-1 sequences in these products. Furthermore, fusion transcripts were not detected by this technique in a series of non-pPNET pediatric solid tumors. Detection of EWS/FLI-1 fusion transcripts by RT-PCR therefore provides a novel adjunctive tool in the diagnosis of pPNETs.