Previous studies have demonstrated conflicting results on the effects of acute exercise on FMD. The aim of the study was to examine brachial artery FMD before and after 3 bouts of acute exercise performed at different intensities. 10 healthy males (mean±SD age: 22±1 years) completed 30 min of cycling at 50, 70 and 85% maximal heart rate (HRmax). Brachial artery FMD and the shear rate area-under-the-curve (cuff deflation to peak dilation; SRAUC) were assessed pre- and immediately post-exercise using high-resolution echo-Doppler. A generalized estimating equation (GEE) analysis was used to estimate the effect magnitudes of exercise intensity and time (pre/post) on FMD, whilst controlling for the influence of baseline diameter and SRAUC. Both baseline diameter and SRAUC were elevated by exercise. With covariate-control of these variables, the decrease in brachial artery FMD was negligible after exercise at 50% HRmax (6.3±2.6 vs. 5.9±2.5%; 95%CI for difference: - 0.59-1.34%) with larger decreases in FMD after exercise at 70% (6.1±1.8 vs. 4.7±1.9%; 95%CI for difference: 0.08-2.58%) and at 85% HRmax (6.6±1.6 vs. 3.6±2.2%; 95%CI: 0.41-5.42%). In conclusion, even after accounting for exercise-mediated changes in shear and baseline diameter, our data indicate that a negative relationship exists between exercise intensity and FMD.