Factors influencing prognosis and long term outcome of thyroid cancer have been described by several groups. It is, however, not clear how the moderate iodine deficiency in Hungary can influence the previously described prognostic factors by other means than shifting differentiated cancer incidence toward the follicular type. Data of 423 out of 472 patients who had been operated on for papillary (372) and follicular (100) thyroid cancer between 1971 and 1997 at our institution have been analyzed retrospectively. Histological specimens were re-evaluated and, if needed, revised. Survival curves were compared using the Kaplan-Meier method. The overall 5 and 10 year survival rates were 93% and 89% for papillary, and 92% and 80% for follicular carcinoma. As an independent factor extrathyroidal invasion (papillary p = 0.000, follicular p = 0.000), lymph node involvement (papillary p = 0.000, follicular 0.011), distant metastases (papillary p = 0.000, follicular p = 0.000), and age over 40 years (papillary p = 0.000, follicular p = 0.000) had negative influence on survival. Multifocality, gender, type of surgery (total or near-total thyroidectomy vs. less than near-total thyroidectomy), and lymphocytic infiltration did not influence survival. Iodine intake did not influence survival, however, the incidence of follicular cancer was higher in iodine deficient regions. When analyzing the papillary and follicular groups separately by Cox regression, extrathyroidal invasion (p = 0.008), lymph node metastasis (p = 0.004), distant metastasis (p = 0.000), and age over 40 years (p = 0.000) were significant predictors in the papillary group, while only tumor extrathyroidal invasion (p = 0.019), and distant metastases (p = 0.000) were significant negative factors in the follicular group.