The objective of the study was to explore the changes in melatonin and zinc levels in rats with induced hypothyroidism. Thirty adult male rats used in the study were allocated to three groups with equal numbers. Group 1: General control group which was not subjected to any procedure. Group 2: Sham-hypothyroidism group to which was administered 10 mg kg-1 intraperitoneal (i.p.) physiologic saline (0.09% NaCl) for 4 weeks. Group 3: Hypothyroidism group which was supplemented with intraperitoneal 10 mg kg -1 propylthiouracil (PTU) for 4 weeks. Blood samples collected from all animals at the end of the study by decapitation were analysed for serum Total T4 (TT4), Total T3 (TT3), Free T4 (FT4), Free T3 (FT3) (ELISA) as well as for melatonin (RIA) hormones and zinc levels (atomic emission). Comparison of the study groups in terms of thyroid hormones, melatonin and zinc levels showed that TT4, TT3, FT4, FT 3, melatonin and zinc levels in group 3 were lower than those in groups 1 and 2 (p < 0.01). These parameters were not different in groups 1 and 2. The results of the study demonstrate that PTU supplementation for 4 weeks results in a significant inhibition in both melatonin and zinc levels. Inhibited melatonin levels may result from the decrease in zinc levels. Copyright © 2006 John Wiley & Sons, Ltd.