Abstract: Objective: To assess the feasibility of detecting the EWS-ATF1 fusion gene and chimeric mRNA inparaffin-embedded clear cell sarcoma (CCS) tissues and to investigate its significance in the diagnosis of CCS. Methods: From 1992 to 2006, paraffin-embedded tumor tissues from 26 cases of CCS and 20 cases of other tumor types were col-lected. EWS-ATF1 fusion transcripts were detected by nested RT-PCR and RT-PCR. β -actin and β ₂ -microglobulin wereused as internal controls. The expression of S-100 and HMB-45 was detected by SP immunohistochemistry in the forma-lin-fixed, paraffin-embedded tumor tissues. Results: Of the clear cell sarcoma samples, 22/26 had detectable expressionof β -actin and 24/26 had detectable expression of β ₂ -microglobulin. EWS-ATF1 fusion transcripts were positive in 20(16type Ⅰ cases, 0 type Ⅱ cases, 4 type Ⅲ cases) of the 24 CCS cases with detectable β ₂ -microglobulin expression. NoEWS-ATF1 mRNA expression was detected in the 20 control samples. The general expression rate of S-100 and HMB-45was 79.2% and 70.8%, respectively. Conclusion: Detection of the EWS-ATF1 fusion gene in formalin-fixed paraffin-embedded materials by nested RT-PCR and RT-PCR is feasible. EWS-ATF1 can be used as a diagnostic index for thediagnosis and differential diagnosis of CCS.