Wearable inertial sensors have undergone great development offering an easy approach to track physical activity for both athletes and for the general public. Their immense potential to assess motion impairment in clinical practice is now fostering research on evaluation protocols, sensor configurations, and significant metrics that could be helpful to evaluate the condition of patients with a motor disease. This systematic review provides a clear picture of the current state-of-art in this research area, outlining the dominant trends, promising opportunities for future work and some guidelines to pursue them. We review Inertial Measurement Unit-based systems that have been used to assess upper limb kinematics in people with acquired neurological disease and neuromuscular disease, over the last 20 years. We evaluate the technological characteristics of the sensors and the clinical contexts in which they have been applied. Finally, we study the biomechanical metrics analyzed in the reviewed papers, focusing on those with clinical relevance to assess and evaluate the motor status of the patients.