Although intralesional calcification is a common finding of synovial sarcoma, ossification is an unusual phenomenon in such a soft tissue sarcoma. Here we report a case of ossifying synovial sarcoma arising in the back of a young adult man. Microscopically, the tumor was composed of spindle or oval cells together with foci of atypical polygonal cells in small nests or cord-like structures, displaying an epithelial appearance. In addition, extensive osteoid or woven bone formation was present in the tumor, resembling extraskeletal osteosarcoma. However, an SS18-SSX1 fusion gene transcript was detected by reverse transcription-polymerase chain reaction, supporting the diagnosis of biphasic synovial sarcoma. The osteogenic phenotype of the tumor cells was further demonstrated by an intense immunohistochemical expression of Runx2, a key transcription factor involved in the regulation of osteoblastic differentiation. The current case suggests the diagnostic utility of the molecular detection of a tumor type-specific fusion gene and expands the phenotypic plasticity of the soft tissue sarcoma of uncertain differentiation.