The aim of the paper is to analyse the epidemiological situation of thyroid cancer in Cracow region from 1986 to 1999 and to review regional thyroid cancer registers in Poland (including 43.7% of the Polish population) in 1999. The standardized register was based upon assumptions: 100% of histopathological verification according to ICD-10, the register ascertainment in at least 80%, the demographic area not smaller than 100,000 inhabitants, the incidence rate (IR) calculated as the newly diagnosed cases number per 100,000 inhabitants in a calendar year. Since 1990 a statistically significant rise of the thyroid cancer incidence affecting mainly women > 40 years of age have been observed. From 1998-1999 the cancer morbidity was reduced. Within the last 5 years in the Cracow area the follicular carcinoma incidence has decreased significantly, which has been associated with effective iodine prophylaxis. The highest incidence values have been observed in Cracow and Olsztyn, showing a territorial relationship with the highest thyroid irradiation doses after Chernobyl accident. The mean IR value has been 3.86 (1.48 men, 6.08 women), which corresponds to about 1500 newly diagnosed cases in Poland in 1999. The follicular to papillary carcinoma ratio has been 5.32. The major etiological factors have been iodine deficiency and ionising radiation. The present data have indicated that iodine prophylaxis should be continued and that the population should be protected against ionising radiation.