The aim of this study was to clarify the genetic alterations in anaplastic transformation of the thyroid cancer. A total of 17 thyroid cancers including 7 anaplastic and 10 papillary cancers were analyzed for loss of heterozygosity (LOH) on chromosome 16p and 18q. All the samples from anaplastic cancer showed LOH at one or more loci out of ten markers on 16p, and only two showed one LOH at two loci out of five markers on 18q. No LOH was found on either 16p or 18q in papillary cancers. D16S423, D16S418 and D16s406 on 16p13.3 were the most frequently deleted loci in anaplastic cancers, and the region around these may harbor the putative tumor suppressor gene related to anaplastic transformation of thyroid cancer.