The reverse transcriptase polymerase chain reaction (RT-PCR) provides a technique to diagnose a group of sarcomas and small round cell tumors that contain specific chromosomal translocations and chimeric gene fusion products. We adapted real-time qualitative RT-PCR to utilize dual-labeled, fluorogenic, TaqMan probes, which hybridize to targets that overlap the junction of the chimeric gene fusions in alveolar rhabdomyosarcoma (ARMS), synovial sarcoma (SS), and desmoplastic small round cell tumor (DSRCT). Assays were confirmed on cell lines and tissue samples; appropriate negative amplification assays were obtained when each tumor-specific probe and primer set was used on different neoplasms and cell lines that were not expected to harbor the specific translocations and chimeric gene fusions. Although our cases are few, we speculate that as more molecular variants of ARMS, SS, and DSRCT are discovered, clinical correlations based on precise molecular features will be required and fusion site specificity will be assured by the use of junction-based TaqMan probes.