The phenomenon of losing a green signal in synovial sarcoma (SS) using the SS18 break-apart probe by fluorescence in situ hybridization (FISH) has been poorly described. In this study, 12 SS with missing a green signal were identified. This series included 7 males and 5 females, aged 17 to 69 years (median, 38.5 years). The tumors involved the extremities (50%), mediastinum (16.7%), hypopharynx (8.3%), neck (8.3%), thyroid (8.3%), and retroperitoneum (8.3%). The tumors were classified as monophasic SS (58.3%) and poorly differentiated SS (41.7%). An anaplastic SS showing features of pleomorphic sarcoma was observed. Immunostaining for TLE1, BCL2, CD99, epithelial membrane antigen, cytokeratin (AE1/AE3), cytokeratin 7, S-100 protein, and CD34 was consistent with typical SS. In FISH, all the tumors showed the pattern of 1 to 3 fused signal(s) with 1 to 3 red signal(s), without corresponding a green signal. The fusion transcripts included SS18-SSX1 (8/10, 80%) and SS18-SSX2 (2/10, 20%) fusions. Median and 5-year overall survival were 19.1 months and 43.6%, respectively. In conclusion, we reported a series of SS losing a green signal in the SS18 FISH assay. We propose that this variant FISH pattern should be interpreted as a peculiar unbalanced rearrangement of the SS18 gene and subsequent SS18-SSX fusion test should be recommended. The cases in this study seem to show some unusual clinicopathological features, including unusual locations, higher proportions of poorly differentiated SS, and aggressive clinical course. However, whether this variant FISH pattern is associated with peculiar clinicopathologic features awaits larger series.