In moderate physical exercise, the transition from predominantly anaerobic towards predominantly aerobic metabolism is a key step to improve performance. Increase in the supply of oxygen and nutrients, such as free fatty acids (FFA) and glucose, which accompanies high blood flow, is required for this transition. The mechanisms involved in the vasodilation in skeletal muscle during physical activity are not completely known yet. In this article, we postulate a role of FFA and heat production in this process. The presence of uncoupling protein‐2 and ‐3 (UCP‐2 and ‐3) in skeletal muscle, whose activity is dependent on FFA, suggests that these metabolites can act as mitochondrial uncouplers in this tissue. Evidence indicates however that UCPs act as uncouplers only when coenzyme Q is predominantly in the reduced state (i.e. under nonphosphorylation conditions or state 4 respiration) as is observed in resting muscles and in the beginning of physical activity (predominantly anaerobic metabolism). The increase in the lipolytic activity in adipose tissue in the beginning of physical activity results in elevated plasma FFA levels. The FFA can then act on the UCPs, increasing the local heat production. We propose that this calorigenic effect of FFA is important to activate nitric oxide synthase, resulting in nitric oxide production and consequent vasodilation. Therefore, FFA would be important mediators for the changes that occur in muscle metabolism during prolonged physical activity, ensuring the appropriate supply of oxygen and nutrients by increasing blood flow at the beginning of exercise in the contracting skeletal muscles. Copyright © 2006 John Wiley & Sons, Ltd.