High resolution ultrasound, combined with computer imaging technology, is commonly used to measure changes in brachial artery diameter for the determination of endothelial-dependent vasodilation (EDD) and endothelial independent-vasodilation (EID). Currently, two methods of computerized edge-detection systems are in use to measure changes in artery diameter. One system involves the sonographer manually tracking the artery walls while the second system involves a computer automated edge-detection system that automatically tracks the artery wall. The purpose of this study was to compare the two types of computerized edge-detection systems for measuring vascular function and structure. One hundred fifty (female = 70, male = 80) participants agreed to participate. Baseline brachial diameter, carotid intima-medial thickness (cIMT), EDD and EID were measured by the two computerized edge-detection systems utilizing the same ultrasound B-mode image. Mean values (+/-standard error) for baseline diameter, cIMT, EDD and EID were 3.53 (+/-0.10) mm, 0.43 (+/-0.01) mm, 5.72 (+/-0.20)% and 22.17 (+/-0.60)%, respectively for the manual edge-detection software system. Mean values for baseline diameter, cIMT, EDD and EID were 3.59 (+/-0.10) mm, 0.44 (+/-0.01) mm, 7.33 (+/-0.30)% and 25.77 (+/-0.60)%, respectively for the automated edge-detection software system. Bland-Altman plots displayed large variations between the two edge-detection methods for assessing cIMT and changes in artery diameter following brachial EDD and EID. The results of the study demonstrate that manual and automated computerized edge-detection systems track dynamic changes in brachial artery diameter and cIMT measures differently. Therefore, caution should be used when comparing research utilizing different computerized edge-detection systems for measuring vascular function and structure.