With synovial sarcoma (SS) of the thorax, being exceptionally rare, its definite diagnosis is difficult, and the optimal therapy has not yet been established. An examination of our patient, a 64-year-old man with SS using a chest roentgenogram showed a large mass with homogeneous density in the lower two-thirds of the left hemithorax. A computed tomographic image of the chest revealed a large, heterogeneous, enhanced mass in the left hemithorax. Histologic examination of the resected tumor tissues suggested monophasic fibrous SS. A fragment of the SYT-SSX1 fusion transcript, which was smaller than the control, was amplified with reverse transcriptase polymerase chain reaction. Direct sequence analyses revealed the fusion between exon 9 of SYT and exon 5 of SSX1 instead of fusion between exon 10 of SYT and exon 6 of SSX1, which is found in most cases. Although the biological and clinical significance of this rare variant is not yet known, our data present another example of the usefulness of molecular analyses for making a definite diagnosis of SS in unusual sites.