Aggressive fibromatosis represents a group of tumors with heterogeneous patterns of biologic behavior. In this study, gene expression in 12 samples of aggressive fibromatosis, as well as that in samples of normal skeletal muscle and a variety of normal tissues, was determined at Gene Logic Inc (Gaithersburg, MD), with the use of Affymetrix GeneChip U_133 arrays containing approximately 33,000 genes. Gene-expression analysis was performed with the Gene Logic Gene Express software system. Differences in gene expression were quantified as the fold change in gene expression between the sets of fibromatosis tissue and normal skeletal muscle. A set of genes was then identified that was significantly overexpressed in aggressive fibromatosis compared with expression in normal muscle. This set of genes was then further examined for expression in a variety of normal tissues. We identified genes that were selectively overexpressed in aggressive fibromatosis compared with expression in 448 samples comprising 16 different nonneoplastic tissues. In particular, ADAM12, WISP-1, SOX-11, and fibroblast activation protein-alpha were uniquely overexpressed in aggressive fibromatosis compared with expression in normal tissues. In addition, the technique of Eisen clustering identified 2 distinct subgroups of aggressive fibromatosis with regard to gene expression. We conclude that gene-expression patterns may be useful in the further classification of subtypes of aggressive fibromatosis and that such classification could have clinical significance.