Down (DS) and Prader-Willi (PWS) syndromes are chromosomal disorders both characterized by obesity, ligament laxity, and hypotonia, the latter associated with gait instability. Although these shared features may justify a common rehabilitation approach, evidence exists that adults with DS and PWS adopt different postural and walking strategies. The development of an instrumented protocol able to describe these strategies and quantify patients’ gait stability in the current clinical routine would be of great benefit for health professionals, allowing them to design personalized rehabilitation programs. This is particularly true for children with DS and PWS, where motor development is dramatically constrained by severe hypotonia and muscle weakness. The aim of this study was, thus, to propose an instrumented protocol, integrated with the clinical routine and based on the use of wearable inertial sensors, to assess gait stability in DS and PWS children.Fifteen children with DS, 11 children with PWS, and 12 typically developing children (CG) were involved in the study. Participants performed a 10-meter walking test while wearing four inertial sensors located at pelvis, sternum, and both distal tibiae levels. Spatiotemporal parameters (walking speed, stride frequency, and stride length) and a set of indices related to gait symmetry and upper-body stability (Root Mean Square, Attenuation Coefficient and Improved Harmonic Ratio) were estimated from pelvis and sternum accelerations. The Gross Motor Functional Measures (GMFM-88) and Intelligence Quotient (IQ Wechsler) were also assessed for each patient. A correlation analysis among the GMFM-88 and IQ scales and the estimated parameters was then performed.Children with DS and PWS exhibit reduced gait symmetry and higher accelerations at pelvis level than CG. While these accelerations are attenuated by about 40% at sternum level in CG and DS, PWS children display significant smaller attenuations, thus reporting reduced gait stability, most likely due to their typical “Trendelenburg gait”. Significant correlations were found between the estimated parameters and the GMFM-88 scale when considering the whole PWS and DS group and the PWS group alone.These results promote the adoption of wearable technology in clinical routines to monitor gait patterns in children with DS and PWS: the proposed protocol allows to markedly characterize patient-specific motor limitations even when clinical assessment scores provide similar results in terms of pathology severity. This protocol could be adopted to support health professionals in designing personalized treatments that, in turn, could help improving patients’ quality of life in terms of both physical and social perspectives.