The stress response results are conflicting in hypothyroidism. Our aim was to investigate the effects of chronic moderate or vigorous exercise on acute stress applied hypothyroid rats. In the study, 200-250g male Sprague-Dawley rats were used. After determination of basal anxiety levels a group of rats were applied intraperitoneally 6-n-propyl-2-thiouracil (PTU 10 mg.kg-1) for 15 days to form hypothyroidism. Some of the rats were exercised on treadmill for 6 weeks, 30min/5day/week (moderate exercise group-MEG) or 60min/5day/week (vigorous exercise group-VEG). Some of the rats did not exercise. At the end of 6 weeks, for acute stress induction water avoidance stress protocol was performed. At the beginning and end of stress inductions anxiety levels were analyzed. At the end of the experiments the rats were decapitated. Lipid peroxidation (LP) and antioxidant glutathione (GSH) levels, myeloperoxidase (MPO) activity which is an indicator of neutrophil infiltration were measured in heart, stomach, liver, small intestine, bladder tissues. Heart, stomach, liver, small intestine, bladder and extensor digitorum longus, soleus and plantaris muscle samples were evaluated histologically. For statistical analysis Student’s t test or ANOVA were used. The MPO, LP, GSH levels of stomach, small intestine, heart and liver tissues were not significantly different than control group in stress applied hypothyroid rats. Although the MPO levels of heart and stomach tissues were increased in hypothyroid MEG compared to control group (p<0.05-0.01), there were not significant difference in the hypothyroid VEG. The increased LP levels in stomach tissue of MEG were declined in hypothyroid MEG (p<0.05). LP levels were increased in small intestine of hypothyroid VEG and heart tissue of VEG compared to control group (p<0.05). Histological analysis and biochemical measurements support each other. According to our results the vigorous exercise was found to be protective from neutrophil infiltration. Additionally, stress induction did not increase the oxidant damage parameters in hypothyroidism. Our results suggest that different intensity of chronic exercise not only increased the oxidant damage parameters in some tissues, but also were protective in variant tissues.