Fine-needle aspiration biopsy-based cytology has become an established and reliable diagnostic preoperative test in the evaluation of thyroid nodules. Despite the high specificity and sensitivity of the method, results might be doubtful in a significant number of cases. Genetic analysis of the aspirates by RT-PCR may contribute, in parallel to the cytology report, to a more precise diagnosis. Prothymosin alpha and parathymosin are two homologous chromatin remodeling proteins essential for cell cycle progression and proliferation of either normal or malignant cells. A semi-quantitative RT-PCR assay was developed to determine prothymosin alpha and parathymosin mRNA expression patterns in thyroid follicular cells obtained from the fine-needle aspiration biopsy specimens of patients diagnosed with simple nodular goitre, follicular adenoma, papillary and follicular well-differentiated carcinomas. Prothymosin alpha and parathymosin mRNA levels were found significantly elevated in well-differentiated carcinomas in relation to adenomas (p<0.05) and goitres (p<0.05), an event possibly linked to the proliferation activity of thyroid follicular cells. Further studies are required to establish prothymosin alpha and parathymosin as diagnostic proliferation markers in thyroid cancer, especially in cases of undetermined cellular morphology of follicular origin which reflect the most common cytohistopathological discrepancies.