Alterations of genomic DNAs in 9 papillary thyroid carcinomas and 3 follicular thyroid adenomas were examined by restriction landmark genomic scanning, a 2-dimensional gel analysis that allows detection of deletions, amplifications and other rearrangements of genomic DNA. DNAs from both thyroid tumors and associated non-tumorous glandular tissues were cleaved with the restriction enzyme NotI end-labeled with P-32 and size-fractionated by 2-dimensional electrophoresis using HinfI in a second digestion. The altered spots in carcinomas and adenomas were compared with those in nontumorous samples. Five and 4 spots were commonly amplified in carcinomas and adenomas, respectively. One amplified spot was apparently specific only for carcinoma and was not detected in any of adenomas examined. In contrast, 12 spots reduced in intensity were frequently observed in tumors, although a subset of 5 were more sporadically affected in adenomas. The results indicate both common and distinct genetic abnormalities occurring in thyroid tumors, which may relate to the different biological behaviors of malignant and benign neoplasms.