Dysfunction of the endothelium and of the arterial wall is well described in patients with atherosclerosis, diabetes, and other risk factors for vascular disease. In recent years, clinical research has focused on elucidating the role of this dysfunction in influencing vascular disease progression. Alteration in the structure of arteries and disruption of the homeostatic functions of the endothelium act as a substrate for end-organ damage and the occurrence of vascular events. Dysfunction of the vascular endothelial cells is probably the earliest event promoting atherosclerotic lesion formation. Therefore, methods capable of assessing endothelial function at a preclinical stage hold potential to refine cardiovascular risk stratification and serve as a guide to monitor the effects of therapeutic interventions. A number of methodologies are currently employed to assess endothelial function, but the optimal approach is not firmly established. In this article, we critically appraise the use of different methodologies employed to study endothelial function as a surrogate marker of future cardiovascular risk.