Angioleiomyoma is a benign soft tissue tumor that usually develops in the subcutis of the lower extremities. It characteristically consists of thick vessel walls formed by proliferating smooth muscle cells, and vascular channels. Very little is known about the molecular cytogenetic changes in angioleiomyoma. In the present study, we employed comparative genomic hybridization (CGH) to identify relative DNA copy number changes in 33 angioleiomyomas using formalin-fixed and paraffin-embedded tumor tissues. CGH results were obtained in 23 (70%) cases. Eight (35%) of the 23 cases exhibited DNA copy number changes involving one or two chromosomes, whereas the remaining 15 cases exhibited no DNA copy number changes. The most common recurrent loss was found in chromosome 22 (the minimal common region was 22q11.2 in five cases). Recurrent gain was seen at Xq (three cases). High-level amplification was not observed. To our knowledge, this is the first report on molecular cytogenetic characterization of angioleiomyomas using CGH from formalin-fixed and paraffin-embedded specimen. The present study has identified chromosomal regions that may contain genes involved in the development of at least some angioleiomyomas.