Purpose To study the expression of FLI-1 and CD99 in small round cell tumor and to explore the utility of FLI-1 in differentiatial diagnosis of small round cell tumor.Methods 46 cases of small round cell tumor were immunohistochemically detected with FLI-1 and CD99,combined with clinical data and pathology.Results The positive expression rate of FLI-1 was 90.5%(19/21) in Ewing's sarcoma/peripheal primitive neuroectodermal tumor(EWS/PNET),14.3%(1/7) in poorly differentiated synovial sarcomas,22.2%(2/9) in rhabdomyosarcomas,0%(0/5) in esthesioneuroblastomas and 0%(0/4) in mesenchymal chondrosarcomas,respectively.But CD99 expression was 95.0%(20/21) in EWS/PNET,71.4%(5/7) in poorly differentiated synovial sarcomas,66.7%(8/9) in rhabdomyosarcomas,75.0%(3/4) in esthesioneuroblastomas and 60%(3/5) in mesenchymal chondrosarcomas,respectively.The sensitivity and specificity of FLI-1 in EWS/PNET were 90.5% and 88%,but those of CD99 in EWS/PNET were 95.0% and 32%,respectively.The specificity of FLI-1 in EWS/PNET was higher than that of CD99(P0.05).Conclusions Immunohistochemical detection of FLI-1 is valuable in the diagnosis of EWS/PNET,and can be reliably applied to the differential diagnosis of small round cell tumors.