Alveolar soft part sarcoma (ASPS) is a rare, histologically distinctive soft tissue sarcoma typically occurring in children and young adults. Although the tumor often shows focal expression of muscle markers, its relationship with rhabdomyosarcoma is not established. The genetic background of ASPS is poorly understood. This study was undertaken to analyze the DNA copy number changes in 13 cases of ASPS using comparative genomic hybridization (CGH) on formaldehyde-fixed, paraffin-embedded tissue sections. Four ASPS cases showed DNA copy number changes. Gains were more common than losses. Gains observed in more than one case included 1q, 8q, 12q and 16p. Although these findings do not show consistent DNA copy number changes in ASPS, they give preliminary clues to genomic areas that might be important in the pathogenesis of ASPS.