This study aims to validate a commercially available inertial sensor based motion capture system, Xsens MVN BIOMECH using its native protocols, against a camera-based motion capture system for the measurement of joint angular kinematics. Performance was evaluated by comparing waveform similarity using range of motion, mean error and a new formulation of the coefficient of multiple correlation (CMC). Three dimensional joint angles of the lower limbs were determined for ten healthy subjects while they performed three daily activities: level walking, stair ascent, and stair descent. Under all three walking conditions, the Xsens system most accurately determined the flexion/extension joint angle (CMC > 0.96) for all joints. The joint angle measurements associated with the other two joint axes had lower correlation including complex CMC values. The poor correlation in the other two joint axes is most likely due to differences in the anatomical frame definition of limb segments used by the Xsens and Optotrak systems. Implementation of a protocol to align these two systems is necessary when comparing joint angle waveforms measured by the Xsens and other motion capture systems.