In inertial motion capture, a multitude of body segments are equipped with inertial sensors, consisting of 3D accelerometers and 3D gyroscopes. Using an optimization-based approach to solve the motion capture problem allows for natural inclusion of biomechanical constraints and for modeling the connection of the body segments at the joint locations. The computational complexity of solving this problem grows both with the length of the data set and with the number of sensors and body segments considered. In this work, we present a scalable and distributed solution to this problem using tailored message passing, capable of exploiting the structure that is inherent in the problem. As a proof-of-concept we apply our algorithm to data from a lower body configuration.