Fine needle aspiration biopsy (FNAB) is the preferred technique for the initial diagnostic evaluation of thyroid lesions, which nevertheless poses a diagnostic challenge for all clinicians involved. The latter necessitates the use of molecular markers on thyroid cytology. MIB-1 is a molecular marker already used in the cytological evaluation of various tumors. In this study, we assessed whether MIB-1 proliferation index adds diagnostic information to the conventional cytological analysis of thyroid nodules and prognostic information in thyroid cancers. MIB-1 index for various thyroid lesions was retrospectively reviewed in a series of 504 patients. Furthermore, the prognostic value of MIB-1 index was investigated for 183 of the patients with papillary thyroid cancer (PTC). MIB-1 index was significantly higher in anaplastic thyroid cancer (ATC) compared to other tumor types (p<0.01). No significant difference in MIB-1 index was observed between thyroid adenomas and follicular carcinomas. In PTC, MIB-1 index equal to or >4% was found to be an independent factor significantly associated with higher risk of distant metastasis and disease-related mortality (p<0.05). Conclusively, this study shows that preoperative MIB-1 index assessment in FNAB of thyroid nodules offers little diagnostic information as far as follicular tumors are concerned. In cases of PTC, though, MIB-1 may serve as a prognostic indicator of disease spreading and poor survival and hence influence the planning of the overall treatment scheme.