Thyroid nodules are frequent and sometimes they pose a diagnostic and prognostic problem. DNA ploidy study and cell cycle analysis could be of value in the distinction between benign tumors and malignant tumors. Formalin-fixed and paraffin-embedded tissues from 69 patients with different benign and neoplastic lesions were investigated. Nuclear DNA content in thyroid cells was measured after Feulgen staining using SAMBA 200 image analysis system. A diploid DNA stemline was revealed in 75% of histologically proven benign thyroid tumors (15/20) and aneuploidy was found in 57.2% of malignant tumors (28/49). There is a significant correlation between aneuploidy and extra-thyroid extension (p=0.007) and bilateral and/or mediastinal lymph node metastasis (p=0.02). In the majority of benign tumors (19/20), the proliferation index was lower than 3% (< or =3%) however, this index value was higher than 3% (>3%) in more than 83% of malignant tumors (41/49) (p<0.001). The S phase fraction analysis revealed that the threshold of 14% divide the near whole of benign and malignant tumors (p<0.001). Our findings show that in follicular lesions, proliferation index and S phase fraction study appears interesting and helpful in the distinction between benign and malignant tumors, and aneuploidy seems more interesting in prognosis evaluation of these tumors.