In recent years, wearable systems based on inertial sensors opened new perspectives for functional motor assessment with respect to the gold standard motion capture systems. The aim of this study was to validate an experimental set-up based on 17 body-worn inertial sensors (Awinda, Xsens, The Netherlands), addressing specific body segments with respect to the state-of-the art system (VICON, Oxford Metrics Ltd., Oxford, UK) to assess upper limb kinematics in obese, with respect to healthy subjects. Twenty-three obese and thirty healthy weight individuals were simultaneously acquainted with the two systems across a set of three tasks for upper limbs (i.e., frontal arm rise, lateral arm rise, and reaching). Root Mean Square error (RMSE) was computed to quantify the differences between the measurements provided by the systems in terms of range of motion (ROM), whilst their agreement was assessed via Pearson's correlation coefficient (PCC) and Bland-Altman (BA) plots. In addition, the signal waveforms were compared via one-dimensional statistical parametrical mapping (SPM) based on a paired t-test and a two-way ANOVA was applied on ROMs. The overall results partially confirmed the correlation and the agreement between the two systems, reporting only a moderate correlation for shoulder principal rotation angle in each task (r~0.40) and for elbow/flexion extension in obese subjects (r = 0.66), whilst no correlation was found for most non-principal rotation angles (r < 0.40). Across the performed tasks, an average RMSE of 34° and 26° was reported in obese and healthy controls, respectively. At the current state, the presence of bias limits the applicability of the inertial-based system in clinics; further research is intended in this context.