We assessed HMGI(Y) gene expression in thyroid tumors, control thyroid tissue and in the blood of patients diagnosed with papillary and follicular thyroid cancers to try to differentiate between malignant and benign disease. HMGI(Y) gene expression was analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) in 60 cases of thyroid tumors. Among this number 11 were diagnosed as papillary carcinoma, 37 as follicular carcinoma, and 12 as follicular adenoma. All carcinoma cases selected for this study were classified according to the tumor, lymph node metastases, distant metastases (TNM) classification. HMGI(Y) gene expression was detected only in follicular carcinomas, whereas in papillary carcinomas, follicular adenomas and control tissues there was no positive reaction. In follicular carcinomas the percentage of positive cases (number of samples with presence of HMGI(Y) gene transcript) was the highest and reached approximately 84. There was no statistical dependence between the presence of HMGI(Y) gene expression and tumor size or the presence of lymph node and distant metastases. HMGI(Y) gene expression was also analyzed in whole blood taken from a selected group of patients diagnosed with papillary or follicular carcinomas. Among follicular carcinomas there were 83% of positive cases, whereas among papillary carcinomas there were only 6%. On the basis of our study, we conclude that HMGI(Y) gene expression analysis could be helpful in differentiation between follicular carcinoma and adenoma.