In the present study, 104 goats with endemic fluorosis, living at the foot of the mountains Agri (Mount Ararat) and Tendurek, were compared with 30 healthy goats to investigate the relationship between the plasma levels of the fluoride ion (F) and the thyroid hormones. In addition to the 104 goats with fluorosis all having dental fluorosis, 1.92% had exostoses in their palpable bones, 19.23% had mastication difficulties with weight loss, 2.88% had nail deformities, and 7.69% had lameness. However, signs of goitre in their necks were not present on inspection and palpation. The plasma F concentration was significantly higher (p < 0.001) in the fluorosis group compared to the control group. The plasma F concentrations tended to be higher in the older animals compared to the younger animals, but not significantly so. Compared to the control group, the serum total thyroxine (TT4) was significantly reduced (p < 0.01) in the fluorosis group. No significant differences between the fluorosis and the control groups were found for the serum concentrations of total triiodotyronine (TT3), free triiodotyronine (FT3), or free thyroxine (FT4). Significant decreases were present in the levels of TT3 (p < 0.01) and FT4 (p < 0.001) in the older goats with fluorosis, 3-5-years-old and > 5-years-old, compared to the younger animals, aged 1-< 3 years.