Using Affymetrix oligonucleotide microarrays, we analyzed mRNA gene expression patterns of 12 primary pediatric rhabdomyosarcomas (RMS) and 11 Ewing's sarcomas (EWS), which belong to the small round blue cell tumors (SRBCTs). Diagnostic classification of these cancers is frequently complicated by the highly similar appearance in routine histology, and additional molecular markers could significantly improve tumor classification. A combination of three independent statistical approaches (t-test, SAM, k-nearest neighborhood analysis) resulted in 101 highly significant probe sets that clearly discriminate between EWS and RMS. We identified novel marker transcripts that have not been previously associated with either RMS or EWS yet, including CITED2, glypican 3 (GPC3), and cyclin D1 (CCND1). Expression levels for selected candidate genes were validated by quantitative real-time reverse-transcription PCR. Furthermore, to identify biologically meaningful trends, functional annotations were assigned to 946 genes differentially expressed between EWS and RMS (t-test). Genes involved in protein biosynthesis (n â«Ű⏠28) and complex assembly (n â«Ű⏠9), lipid metabolism (n â«Ű⏠23), energy generation (n â«Ű⏠22), and mRNA processing (n â«Ű⏠11) were expressed significantly higher in EWS. Thus, functional annotation of tumor-specific genes reveals detailed insights into tumor biology and differentiation-specific expression patterns and gives important clues related to the possible cellular origin of these pediatric tumors. Small round blue cell tumors (SRBCTs) are frequently difficult to distinguish by standard histology or, sometimes, even by immunohistochemistry. Rhabdomyosarcoma (RMS) and Ewing's sarcomas (EWS) are common pediatric solid tumors that belong to this group that also includes neuroblastoma and Burkitt's lymphoma. However, the correct diagnosis of SRBCT tumors is essential since treatment regimens, response to therapy and prognosis may differ markedly. Therefore, molecular techniques are increasingly implemented for the diagnostic distinction of SRBCT tumors, including EWS and RMS. Progress in recent years includes the identification of characteristic tumor-specific chromosomal translocations, resulting in the expression of aberrant, oncogenic fusion proteins.RMS is the most common pediatric soft tissue sarcoma and can be histologically subdivided into the more prevalent embryonal (eRMS) and the more aggressive alveolar rhabdomyosarcoma (aRMS). ARMS have an unfavorable prognosis due to a tendency to early relapses and frequent failure of chemotherapy. This is reflected by 5-year survival rates ranging between 20 -50%. Most aRMS express PAX3-FKHR or PAX7-FKHR fusion proteins resulting from [t(2;13)(q35;q14)] or [t(1;13)(p36;q14)] translocations, respectively. 1-3 Although a frequently affected chromosomal locus in eRMS has been defined (11p15.5), specific gene(s) or a fusion transcript have not been identified. 4 Ewing's sarcomas (EWS) and the related, more differentiated peripheral neuroectodermal tumors (PNET) are...