Functional alterations to the endothelial cells of the vascular system may contribute to the improved circulatory performance induced by physical conditioning. We evaluated microvascular reactivity to iontophoretic application of acetylcholine (ACh) and sodium nitroprusside (SNP) through the skin and blood perfusion measurements in the same area using laser Doppler flowmetry. Whereas ACh acts on smooth muscle cells of the vascular system via the production of vasodilator substances from the endothelium, SNP is an endothelium-independent vasodilator acting on vascular smooth muscle cells directly. The study was performed using two groups of subjects with different levels of aerobic endurance, long distance runners competing at national level (n = 9) and controls (n = 9). The subjects were tested for 40 min on a treadmill before and after an exercise test at 80% of their maximal oxygen uptake. During stimulation by ACh cutaneous perfusion increased to a higher level in the athletes than in the controls (overall P < 0.05), whereas an acute period of exercise abolished this difference (overall P > 0.6). There was no significant difference between the athletes and the controls with respect to the SNP-induced increase in cutaneous perfusion either before (P > 0.9) or after (P > 0.9) exercise. The higher cutaneous perfusion responses to stimulation with ACh in the athletes than in the controls may support the hypothesis that regular exercise modifies the responsiveness of the cutaneous endothelium. The difference in ACh-induced perfusion and in unstimulated forearm perfusion between the two groups was present only at rest. This finding indicated that mechanisms were introduced during exercise, which compensated for the lower endothelial sensitivity to stimulation in the controls at rest.