It is not uniformly agreed whether gastrointestinal stromal tumors (GISTs) are phenotypical variants of leiomyomas (cellular leiomyomas) or whether they represent a separate, genotypically definable entity. In an attempt to solve this question, we examined immunohistochemically defined leiomyomas from the esophagus and uterus, gastric schwannomas, and benign gastrointestinal stromal tumors (GIST) by comparative genomic hybridization (CGH). All 14 leiomyomas (nine esophageal, five uterine) were actin- and desmin-positive but negative for CD34 and S100-protein. Changes in DNA copy numbers were seen only in three esophageal leiomyomas. Gains were observed in chromosomes 3, 4, 5, 8, and 17, whereas losses were seen in 16p. All schwannomas were positive for S100-protein and negative for actin, desmin, and CD34. In schwannomas, the only change by CGH was a gain in 11q in one case. The benign GISTs, all from the stomach, were positive for CD34 but negative for desmin and S100-protein; two cases were positive for actin. The CGH findings in the GISTs differed markedly from those in leiomyomas and schwannomas. Ten of the 13 cases (77%) showed DNA copy number losses in 14q, and additional or other losses were found in eight cases, most often in chromosome 22 (seven cases), 15 (three cases), and 1p (two cases). Furthermore, two of the GISTs showed gains in 5q. These results indicate that phenotypically undifferentiated GISTs are also genetically different from leiomyomas and schwannomas and support their classification apart from leiomyomas.