US-guided fine needle aspiration cytology is currently the best diagnostic tool for thyroid nodules. However, it is not sensitive and specific enough for differentiating between benign and malignant follicular tumors. A potentially useful marker for this differentiation is the PAX8-PPARgamma rearrangement, identified in follicular thyroid carcinomas, but not in follicular adenomas or other types of thyroid tumors. The aim of this research was to determine the clinical significance of the PAX8-PPARgamma oncogene in diagnostics follicular thyroid tumors. The study included 62 patients with follicular or Hürthle cell tumors. Gene expression was determined by reverse transcription-polymerase chain reaction (RT-PCR) from paraffin embedded tissues, and PCR products were checked using the agarose gel electrophoresis. The immunohistochemical analysis was performed on archive paraffin embedded tissues with the monoclonal PPARgamma antibody. The statistical analysis has indicated that neither the expression of PAX8-PPARgamma mRNA, nor the immunohystochemical analysis with the PPARgamma antibody correlate with the patohystological diagnosis. The oncogene, PAX8-PPARgamma has not met the expectations as a reliable tumor marker for differentiation between benign and malignant thyroid tumors, which makes the only reliable histological criteria--capsular and vascular invasion.