Background: exercise conditions can affect the expression of genes. Our study investigated the effects of acute and chronic exercise on the expression of genes related to oxidative stress (Tfam, UCP2, UCP3) and immune system (IL-1α, IL-1β, IL-2, IL-8, IL12A, IL12B, TLR2, TLR4). Methods: was formed with 24 people: 12 healthy females and 12 healthy males. Maximal oxygen use capacities of the participants were determined by the Bruce test protocol at the beginning and end of the 8week training program. After calculating their maximal oxygen use capacity, each participant was given an acute running exercise on the tread mill at the speed and incline that the participant would reach to his/her maxVO2 until exhausted. The same people was built to continuous runs (50-70 %) for 8 weeks in a week, and two days of intermediate interval training program (80% and above). Venous blood samples were taken before and after acute exercise with immediately after chronic exercises. RNA isolation was performed using TRIzol Reagent from peripheral blood mononuclear cells. Gene expression was determined by Biomark Real-Time PCR (RT-PCR). Comparisons were performed by using two independent sample t-test and Mann-Whitney U for quantitative data and calculated gene expression values. The statistical significance level was taken as p <0,05. Results: we found that acute exercise in women changed Tfam gene expression (p <0,05). Chronic exercise changes the expression level of more genes (Tfam, IL-1β, TLR4) in women (p<0.05, p<0.001). There was only difference in Tfam gene in males (p <0,05). Conclusions: changes in gene expression differed by sex in exercise. Our results indicate that different workout programs for females and males cause genes to work and they have a positive effect on their expressions and thus increase the efficiency of the exercise.