The aim of the study was to evaluate the correlation between incidence rate (IR) of thyroid cancer and severity of iodine deficiency. The influence of iodine prophylaxis on IR was also investigated. The suspension of iodine prophylaxis in 1980 resulted in goitre prevalence increase in schoolchildren (up to 60%) and elevated TSH levels in neonates observed in early 1990-ties. In 1990 rise in thyroid cancer IR was observed. IR of papillary and follicular carcinoma in 1995 were 1.6 and 1.5 respectively. Papillary to follicular ratio was about 1.0. Such a high prevalence of follicular cancer was specific for iodine deficient regions. In 1997, after introduction of mandatory model of iodine prophylaxis in Poland, increase in papillary thyroid cancer IR was observed, reaching in 1998 6.23 per 100,000 inhabitants. Papillary to follicular cancer ratio rose to 2.48. In 1999 no further increase in thyroid cancer IR was observed. Increase in papillary cancer incidence between 1990 and 1999 may be related to overlapping of iodine deficiency and other cancer risk factors i.e. radiation after Chernobyl accident.