Nodular thyroid disease is a very common disorder with a low frequency of malignancy. The most accurate diagnostic test is fine needle aspiration biopsy (FNAB) of nodules with cytological analysis of the sample. However, this procedure has some limitations in the diagnosis of follicular and papillary thyroid carcinoma. Aim: To detect mRNA from specific malignancy markers in thyroid nodules and to evaluate their potential correlation with cytological and pathological diagnosis. Patients and methods: In 20 patients with thyroid nodules FNAB was performed prior to surgery. The main part of the FNAB sample was used to perform classical cytology. In the remaining of the sample were detected MUC-1, CD26, galectin-3 and TSH receptor mRNAs by RT-PCR technique. Results: Eight patients had positive cytology for papillary cancer; which was confirmed by pathology. Nine had suspicious or non conclusive cytological findings and 3 were negative for neoplastic cells; all 12 were pathologically benign. We detected TSH receptor and galectin-3 mRNA in almost all benign and malignant nodules. MUC-1 was present in 5/8 papillary carcinoma (62.5%), and 1/12 benign nodules (8.3%). CD26 was detected in 7/8 papillary carcinomas but also in 8/12 benign nodules. Conclusions: RT-PCR can be performed in very small samples of thyroid tissue to detect several mRNA markers. MUC-1 can be a potentially useful marker of malignancy in thyroid nodules. It can be detected by RT-PCR as a complementary technique in the diagnostic evaluation of thyroid nodules