In the four major Eastern Boundary Upwelling Systems (EBUS), mesoscale eddies are known to modulate the biological productivity and transport near‐coastal seawater properties toward the offshore ocean, however little is known about their main characteristics and vertical structure. This study combines 10 years of satellite‐altimetry data and Argo float profiles of temperature and salinity, and our main goals are (i) to describe the main surface characteristics of long‐lived eddies formed in each EBUS and their evolution, and (ii) to depict the main vertical structure of the eddy‐types that coexist in these regions. A clustering analysis of the Argo profiles surfacing within the long‐lived eddies of each EBUS allows us to determine the proportion of surface and subsurface‐intensified eddies in each region, and to describe their vertical structure in terms of temperature, salinity and dynamic height anomalies. In the Peru‐Chile Upwelling System, 55% of the sampled anticyclonic eddies (AEs) have subsurface‐intensified maximum temperature and salinity anomalies below the seasonal pycnocline, whereas 88% of the cyclonic eddies (CEs) are surface‐intensified. In the California Upwelling System, only 30% of the AEs are subsurface‐intensified and all of the CEs show maximum anomalies above the pycnocline. In the Canary Upwelling System, ∼40% of the AEs and ∼60% of the CEs are subsurface‐intensified with maximum anomalies extending down to 800 m depth. Finally, the Benguela Upwelling System tends to generate ∼40–50% of weak surface‐intensified eddies and ∼50–60% of much stronger subsurface‐intensified eddies with a clear geographical distribution. The mechanisms involved in the observed eddy vertical shapes are discussed.