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Introduction: Female and male rats response differently to stress and these differences should be taken into account then extrapolation on human population are made. However, the most animal studies are done on male rats and a few on female. The aim of our study was to compare effects of intermittent fasting (IF) on autonomic nervous system balance and antioxidant defense system. Materials and Methods: The experiment was done on female (n=22) and male (n=27) Wistar rats. Animals from control group were fed ad libitum; rats from experimental group have been performing IF for 4 days (get food for 1 hour a day). ECG registration, blood and liver sampling were taken on 4th day of IF. The ECG registration were performed after recovery period (ad libitum conditions for 7 days). Results. RMSSD increased significantly in female rats only by 55% (p=0.011) in the end of IF; effect vanished after recovery; SI was decreased by 138% (p=0.025) only in male rats in the end of IF. Catalase (by 24%, p=0.026) and superoxide dismutase (by 24%, p=0.015) in blood plasma were decreased in female. Ceruloplasmin in blood for both sexes were statistically increased (by 18.5%, p=0.02 for female and by 32.5% p=0.003 for male). Conclusions. Parasympathetic nervous system in female (RMSSD increased) and sympathetic in male (SI decreased) change heart rate due to IF. Increased catalase and superoxide dismutase in females marks inflammation. Ceruloplasmin (important protein for iron exchange) was increased in both sexes, which mark iron metabolism changes.