Background: Use of predominantly anaerobic energy systems such as that seen in 800-meter athlete runners disrupts mitochondrial function as an energy source. Furthermore, it produces free radical substances and causes myocyte damage. Malondialdehyde (MDA) plasma concentrations correlate with free radical levels and are therefore predictive of cell damage. Objective: To analyse the effect of flavonoid antioxidant from chocolate bean extract for prevention of lipid peroxidation of myocyte membranes caused by free radical substances in athletes partaking in predominantly anaerobic sports. Materials and Methods: The study of population consisted of 16 junior athletes who compete in 800-meter races. This was a randomized experimental study. Subjects were divided into two groups, chocolate bean extracts and placebo groups, and then practiced regularly for 14 days. All subjects were assessed on day 15. Results were analysed statistically using paired t test, ANOVA and Duncan tests. Results: Concentrations of MDA were reduced in flavonoid group. Conclusion: Flavonoid antioxidant from chocolate bean extract may prevent myocyte damage was caused by reperfusion injury.