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This study compares the reliability and reproducibility of flow-mediated dilatation (FMD) and peripheral arterial tonometry (PAT) to assess endothelial function. Eighteen volunteers with coronary heart disease underwent simultaneous testing of FMD by means of brachial artery ultrasound scanning and PAT with the EndoPAT 2000. The subjects underwent both tests twice with an interval of 30 minutes and the same protocol was repeated 2 days later. The within-day variability was lower for the FMD measurements than for the PAT measurements (10% versus 18%; p < 0.05). The between-day variability was similar (11%). A significant correlation was found between PAT and FMD (r = 0.57, p < 0.001). The typical errors of measurements for FMD were lower than those for PAT. In conclusion, in this study, FMD demonstrated the best reliability for the within- and between-day and separate day measurements when compared to PAT.