Numerous studies aimed at the identification of chromosomal regions that are frequently deleted in specific tumor types have pointed to the location and involvement of specific tumor suppressor genes. Previous studies of loss of heterozygosity (LOH) among thyroid tumors have revealed frequent allelic deletions at a few chromosomal regions. A systematic genome-wide examination of LOH in a substantial number of follicular carcinomas, however, has not been performed previously. We assessed LOH at polymorphic markers from each nonacrocentric autosomal arm in a panel of 28 follicular thyroid carcinoma tumor and normal pairs. In contrast to the results of previous allelotype studies, we found high rates of LOH at multiple chromosomal regions. The highest rate of loss in our study was at 2p (50.0%), and 2q (50.0%), and the mean rate of LOH was 20.4%. Marked genetic instability in a subset of tumors was demonstrated by high fractional allelic loss, which accounted for more than 80% of observed LOH in this study. High fractional allelic loss was significantly associated with oxyphilic features and poor differentiation of these tumors. Our data provide evidence of a prevalent phenotype of nondisjunctional whole chromosomal loss in follicular thyroid carcinomas.