The purpose of our study was to assess microinvasion in a case of synovial sarcoma by means of the reverse transcriptase polymerase chain reaction (RT-PCR) for detecting SYT-SSX fusion transcripts. Furthermore, we tried to compare the RT-PCR results with those obtained by conventional histopathological examination. A 45-year-old man with synovial sarcoma in the left lower leg underwent above-knee amputation and partial resection of the right lung because of local recurrence and metastasis to the lung. We obtained samples from the tumor and from locations at distances of 1, 3, and 5 cm from the tumor margin in the amputated limb. Samples were also obtained from the resected pulmonary tumor and peripheral blood. SYT-SSX1 chimeric genes could be detected in the samples obtained from up to 3 cm outside the tumor by RT-PCR. Histopathological examination confirmed tumor cells up to 1 cm from the tumor margin. We believe that using a molecular assay in addition to a histopathological examination provides a more sensitive and accurate assessment of the surgical margin.