Type 1 and type 2 iodothyronine 5' deiodinases (D1 and D2, respectively) catalyze the conversion of thyroxine (T(4)) to triiodothyronine (T(3)). Similar to other genes crucial for T(3) generation, D1 and D2 expression might be disturbed in papillary thyroid cancer (PTC) possible as a result of impairments in thyroid transcription factors Titf1/Nkx2-1 and Pax-8. The aim of the study was to investigate changes in the expression of D1 and D2 in PTC compared to changes in the expression of Titf1/Nkx2-1 and Pax-8. Although D1 and D2 activities were decreased in tumor samples (PTC) compared to control C samples (tissues from a nontumorous part of the gland), the differences were not statistically significant. Contrary to that, their mRNA levels were significantly decreased in PTC samples compared to C samples (p = 0.017 and p = 0.012, respectively). Interestingly there was clear discrepancy between enzymatic activity and mRNA level of both deiodinases. There was a statistically significant correlation between D1 and Pax-8 (r = 0.464, p = 0.039), D2 and Pax-8 (r = 0.461, p = 0.041), D2 and Titf1/Nkx2-1 mRNA levels (r = 0.526, p = 0.017). Our results show that changes in D1 and D2 expression in PTC, including the discrepancy between deiodinases activity and mRNA level, might possibly related to impaired Titf1/Nkx2-1 and Pax-8 action.