Ewing sarcoma and related neoplasias are characterized by the presence of specific chromosomal translocations resulting in EWS/ETS gene rearrangements. Created EWS/ETS-oncogene fusion transcripts can be detected in up to 98% of ESFT and provide tumour-specific markers useful in diagnostics. Using RT-PCR for detection of this aberration we can reveal minimal amounts of tumour cells contaminating BM, blood or apheresis products. We have examined BM samples from 22 patients (21 newly diagnosed and one recurrent disease) with histologically confirmed ESFT for the presence of contaminating tumour cells in BM at the time of diagnosis. Sixteen patients presented with localized disease, six had distant metastases at the first presentation. Ewing sarcoma cells were detected in the BM of 5/16 (31%) patients with localized disease and 3/6 (50%) with clinically detectable metastases at diagnosis. BM smears prepared from the same aspirates evaluated by light microscopy were all negative, even in two patients with multiple bone disease. We have confirmed the high sensitivity of the RT-PCR assay for detection of minimal BM infiltration in localized and metastatic ESFT. We have found that more than a quarter of patients with localized ESFT have minimal BM infiltration. Although the clinical significance of the minimal disease detected at the molecular level remains unknown, RT-PCR evaluation may enable better stratification of patients into risk groups in the future.