Gastrointestinal stromal tumors (GISTs), also referred to as "gastrointestinal pacemaker cell tumors (GIPACT)" are mesenchymal neoplasms that are phenotypically similar to the interstitial cells of Cajal (ICC). Cytogenetic studies of this entity are rare and molecular cytogenetic studies utilizing chromosome-specific probes are nonexistent. In the current study, cytogenetic and molecular cytogenetic analysis of 12 histologically and immunohistochemically confirmed GISTs revealed loss of a whole chromosome 14 or region(s) of 14q in 8 tumors evaluated (67%) and loss of a whole chromosome 22 or region(s) of 22q in 8 (67%) patients. Loss of 14q and 22q were observed in histologically benign and malignant GISTs. Structural rearrangements of chromosome 1 were observed in 2 malignant GISTs. These findings indicate that loss of 14q and 22q are nonrandom, early events in GIST tumorigenesis and suggest that tumor suppressor genes responsible for the development of this neoplasm may be located on these chromosomal arms.