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Brachial artery flow-mediated dilation (FMD) is associated with risk factors providing information on cardiovascular prognosis. Despite the large effort to standardize the methodology, the FMD examination is still characterized by problems of reproducibility and reliability that can be partially overcome with the use of automatic systems. We developed real-time software for the assessment of brachial FMD (FMD Studio, Institute of Clinical Physiology, Pisa, Italy) from ultrasound images. The aim of this study is to compare our system with another automatic method (Brachial Analyzer, MIA LLC, IA, USA) which is currently considered as a reference method in FMD assessment.The agreement between systems was assessed as follows. Protocol 1: Mean baseline (Basal), maximal (Max) brachial artery diameter after forearm ischemia and FMD, calculated as maximal percentage diameter increase, have been evaluated in 60 recorded FMD sequences. Protocol 2: Values of diameter and FMD have been evaluated in 618 frames extracted from 12 sequences.All biases are negligible and standard deviations of the differences are satisfactory (protocol 1: −0.27 ± 0.59%; protocol 2: −0.26 ± 0.61%) for FMD measurements. Analysis times were reduced (−33%) when FMD Studio is used. Rejected examinations due to the poor quality were 2% with the FMD Studio and 5% with the Brachial Analyzer.In conclusion, the compared systems show a optimal grade of agreement and they can be used interchangeably. Thus, the use of a system characterized by real-time functionalities could represent a referral method for assessing endothelial function in clinical trials.