Background: It remains to be established to what extent physical activity (PA) levels among individuals are independently associated with deviations from the “optimal” state of the arterial system. Accelerometers have been proposed as means to obtain reliable, objective, and more comprehensive data of PA. Decisions at the time of data collection/processing could influence the association between accelerometry-derived indices and arterial properties.Objectives: (i) To identify to what extent the strength of association between arterial properties and accelerometer-derived indices depend on the recording site and/or the epoch length; (ii) to determine whether some arterial characteristics (hemodynamic vs. structural vs. functional) or regions (elastic vs. transitional vs. muscular arteries; central vs. peripheral) have higher levels of association with accelerometry-derived indices.Methods: Physical activity (PA), cardiovascular risk factors (CRFs), and cardiovascular properties were evaluated in 60 volunteers (general population; age: 23–62 years; women: 43%). PA was measured daily for 7 days (free-living situation; triaxial-accelerometers ActiGraph-GT3X+; hip and wrist; “Worn-to-wrist” option) and raw data was converted at epoch lengths of 1, 5, 10, 30, and 60-s. PA-related energy expenditure, daily time in moderate-to-vigorous PA, steps/minute, and counts-per-minute for vector magnitude were calculated. The cardiovascular evaluation included hemodynamic (central and peripheral pressure), structural (diameters and intima-media thickness), and functional (local and regional stiffness) parameters of carotids, femoral, and brachial arteries, and carotid-femoral and carotid-radial pathways. Arterial z-scores were obtained using age-related equations derived from healthy participants not exposed to CRFs (n = 1,688; age: 2–84 years; female: 51.2%) to evaluate at which degree each parameter deviates from the “optimal” value.Methods: In general, hip recordings outperformed those obtained on the wrist regarding the strength of association with arterial parameters. Accelerometer-derived indices and their association with arterial properties vary depending on the recording site and epoch length. PA indices are stronger associated with functional (local) than structural variables and with central than peripheral arteries.Conclusions: Regardless of the PA index, there were independent associations with central artery characteristics, which reinforces that these territories would be the most related to PA levels. Differences in data acquisition and processing could lead to differences in conclusions when addressing the association between accelerometer-derived indices and the cardiovascular system.