Adult soft tissue sarcomas are a heterogeneous group of tumors, including well-described subtypes by histological and genotypic criteria, and pleomorphic tumors typically characterized by non-recurrent genetic aberrations and karyotypic heterogeneity. The latter pose a diagnostic challenge, even to experienced pathologists. We proposed that gene expression profiling in soft tissue sarcoma would identify a genomicbased classification scheme that is useful in diagnosis. RNA samples from 51 pathologically confirmed cases, representing nine different histological subtypes of adult soft tissue sarcoma, were examined using the Affymetrix U95A GeneChip. Statistical tests were performed on experimental groups identified by cluster analysis, to find discriminating genes that could subsequently be applied in a support vector machine algorithm. Synovial sarcomas, round-cell/myxoid liposarcomas, clear-cell sarcomas and gastrointestinal stromal tumors displayed remarkably distinct and homogenous gene expression profiles. Pleomorphic tumors were heterogeneous. Notably , a subset of malignant fibrous histiocytomas , a controversial histological subtype , was identified as a distinct genomic group. The support vector machine algorithm supported a genomic basis for diagnosis, with both high sensitivity and specificity. In conclusion, we showed gene expression profiling to be useful in classification and diagnosis, providing insights into pathogenesis and pointing to potential new therapeutic targets of soft tissue sarcoma. cases. 1 There are over 50 subtypes of this disease, which are currently diagnosed by genetic and morphological criteria. 2,3 Those most frequently seen include liposarcoma, leiomyosarcoma, malignant fibrous histiocytoma (MFH), fibrosarcoma, and synovial sarcoma. 4 The molecular classification of STS includes two major categories on the basis of 1) a single recurrent genetic alteration, such as chromosomal translocations (synovial sarcoma, myxoid/round-cell liposarcoma, clear-cell sarcoma) or activating mutation (KIT), or 2) non-recurrent genetic aberrations, which form part of a complex abnormal karyotype. 5 It is possible to classify some STS by their recurrent chromosomal translocations or somatic mutation, 6 such as the presence of SYT-SSX fusion transcript in synovial sarcoma, 7,8 EWS-ATF1 in clear-cell sarcoma, 9,10 TLS-CHOP in myxoid/round-cell liposarcoma 11,12 and ASPL-TFE3 in alveolar soft-part sarcoma. 13 Most of these translocations produce chimeric transcription factors, which presumably deregulate the expression of several target genes. 14 In the case of gastrointestinal stromal tumors (GIST), a distinct somatic mutation has been described in KIT, 15-17 which leads to ligand-independent constitutive activation of its encoded receptor tyrosine kinase. This in turn results in altered cell proliferation and tumorigenesis.The group of tumors characterized by numerous, nonrecurrent chromosomal alterations includes MFH, conventional fibrosarcoma, leiomyosarcoma, de-differentiated liposarcoma and pleomo...