This study aimed to evaluate the diagnostic value of SYT-SSX detected by reverse transcriptase-polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) for synovial sarcoma (SS) in known and potential cases. SYT-SSX was analyzed in formalin-fixed, paraffin-embedded tissues of 62 known SS, 60 non-SS and 133 potential SS by RT-PCR and FISH. FISH was mainly performed on a tissue microarray with some modifications. SYT-SSX was detected in 94.7% (54/57) of known SS and 70.5% (86/122) of potential SS by RT-PCR and in 96.7% (58/60) of known SS and 78.1% (100/128) of potential SS by FISH. Moreover, SYT-SSX was negative in 100% (58/58) of non-SS by RT-PCR and in 100% (59/59) of non-SS by FISH. Accordingly, SYT-SSX was detected in 106 potential SS by RT-PCR or FISH, including 80 cases manifested by both methods, 20 specimens verified only by FISH and 6 samples confirmed only by RT-PCR. Clinical findings and immunohistochemistry data were analyzed in potential SS with final molecular diagnosis. The positive ratio of cytokeratin (CK) and epithelial membrane antigen (EMA) in finally diagnosed SS was 51.9% (55/106) and 61.3% (65/106), respectively. Except EMA, clinical parameters (age, sex, tumor size, tumor sites) and other immunohistochemistry indexes (CK, S-100, neurone specific enolase (NSE), CD99, myoglobin, smooth muscle actin (SMA), cluster of differentiation (CD) 68 and mesothelial cell) had no significant difference between finally diagnosed SS and non-SS. It is indicated that the efficiency of FISH is comparable to or even higher than that of RT-PCR for SYT-SSX detection. The detection of SYT-SSX by RT-PCR or FISH is very useful for the final diagnosis of potential synovial sarcomas.