A low-cost inertial measurement unit has been developed for accurate motion capture, allowing real-time spatial position registration (linear and angular) of the user’s whole-body. For this, we implemented a dedicated circuit for 9 degrees of freedom motion sensors, composed of an accelerometer, gyroscope and a magnetometer. We also applied signal processing and data fusion algorithms to prevent the inherent drift of the position signal. This drift is known to exist during the sensor integration process and the implemented algorithms showed promising results. This system is meant to be used in two specific biomedical applications. The first one is linked to the development of a low-cost system for gait analysis of the whole-body, which can be used in home-based rehabilitation systems. The second application is related to the real-time analysis of working postures and the identification of ergonomic risk factors for musculoskeletal disorders.