Background: There are many conflicting opinions regarding the effects of hypoxia on thyroid hormones in different situations. This study evaluates the effect of exercise-induced hypoxia on thyroid hormones and thyroid-stimulating hormone (TSH) in trained young men. Materials and Methods: The participants consisted of 17 healthy men, aged 20-24 years, with mean maximal oxygen uptake and body mass index of 48.6 ± 3.96 ml/kg/min and 21.6 ± 0.91 kg/m 2 , respectively. They did 30-min running on treadmill, at the intensity of 70% of maximal heart rate, in normoxia and three different levels of simulated hypoxic conditions at 2750, 3250, and 3750 m heights. The sessions were interspaced with 72-hour resting breaks. Blood samples for hormonal assays were obtained before exercise and at 0 h and 1 h after exercise. Results: Data analysis, using mixed models, showed no statistically significant hormonal difference among the hypoxic conditions (P > 0.05) except increased thyroxin levels following exercise in all sessions , which were significant only in normoxia and 2750 m height (P < 0.05), without any significant changes in serum triiodotyronine and TSH. Conclusion: With respect to different reports surrounding the effects of high-altitude-induced hypoxia on pituitary-thyroid axis (including stimulatory, inhibitory, or changeless effects), this study revealed only significant increased thyroxin level at 1200 (normoxia) and 2750 m heights, following exercise. These contradictory findings may be attributed to the degree of prescribed hypoxia, planning of natural or simulated height, activity level and type, and study duration. However, for a precise conclusion, further research is recommended.