Characteristic chromosome aberrations and the rearranged genes resulting in chimeric fusion genes have been reported in some bone and soft tissue tumors; t(X; 18) in synovial sarcoma, t(11; 22) in Ewing's sarcoma and primitive neuroectodermal tumor, and t(2; 13) in alveolar rhabdomyosarcoma. We practically used the chromosome analysis and the reverse transcription-polymerase chain reaction (PCR) method as a tool for diagnosis and follow up. All of 10 cases of synovial sarcoma had a chimeric product of SYT/SSX gene. Eleven cases of Ewing's sarcoma and primitive neuroectodermal tumor showed 6 variants of chimeric products between EWS gene and Fli1 gene in the PCR-directed sequence analysis. Although PAX3/FKHD or PAX7/FKHD transcripts were amplified in alveolar rhabdomyosarcoma cases, MyoD1 and myogenin gene which are myogenic transcription factor were also expressed in most rhabdomyosarcomas. These findings indicate that molecular biological analysis may be a useful supplementary method for pathologic diagnosis of bone and soft tissue tumors.