Background: The objective of study was to examine the impacts of exercise training on cardiac, hepatic and plasma brain-derived neurotrophic factor (BDNF) and irisin levels in young and aged rats. Materials and methods: Four-month-old (young) and 20-month-old (aged) female rats performed exercise training consisting of voluntary wheel running for 12 weeks. BDNF and irisin levels were analyzed in the heart, liver and plasma samples by using commercially available enzyme-linked immunosorbent assay (ELISA) kits. Results: Cardiac, hepatic and plasma BDNF levels were lower in the aged sedentary rats, than in the young exercised and aged exercised rats (p < 0.05). Heart, liver and plasma irisin concentrations were lower in the aged sedentary group than in the young sedentary, young exercised and aged exercised groups (p < 0.05) and regular exercise increased irisin levels in all the analyzed tissues when compared to the sedentary counterparts (p < 0.05). Conclusions: The current results show that regular exercise improves aging-induced decrease in the cardiac, hepatic and plasma BNDF and irisin levels.