Gastrointestinal stromal/smooth muscle tumors are uncommon neoplasms for which current criteria for diagnosing malignancy (size and mitotic index) sometimes fail to predict outcome. Cytogenetic studies reveal frequent chromosome 1 abnormalities in these tumors, but significant underlying molecular changes have not been elucidated, and their significance is unknown. DNA was obtained from the formalin-fixed, paraffin-embedded tissue of 80 gastrointestinal stromal/smooth muscle tumors. Tumors were topographically microdissected from surrounding normal tissue; microsatellite markers from tumor and normal tissue were amplified by PCR in the regions of chromosome 1p36 (D1S199, D1S228, D1S450, D1S214, D1S243), 1p12 (D1S418),1p13 (D1S252, D1S514), and 1q32(D1S103). The presence or absence of heterozygosity for each case was mapped at each informative marker. Relationships among loss of heterozygosity (LOH), tumor size, mitotic index, and survival were investigated using correlation analysis, Kaplan-Meier plots, and the Cox model. LOH at 1p36 was found in 24 of 80 cases, suggesting the possibility of a tumor suppressor gene at 1 p36 near the site of a suspected neuroblastoma tumor suppressor gene. Patients whose tumors demonstrated LOH at 1 p36 had significantly shorter survival (p = 0.017) than those whose tumors did not. LOH at 1 p36 retained independent prognostic significance in a multivariate model that included KIT mutation status and tumor size; the mitotic index, however, did not retain independent significance in such a model. LOH was observed at 1 p12-1p13 (most frequently at 1p13.3) in 19 of 80 cases, but loss of heterozygosity at this site did not influence survival. No LOH was observed near 1q32. These findings provide strong evidence for a prognostically significant tumor suppressor gene in the region of chromosome 1p36.3.