This paper presents an inertial based sensing system for real-time three-dimensional measurement of human spinal motion, in a portable and non-invasive manner. Applications of the proposed system range from diagnosis of spine injury to postural monitoring, on-field as well as in the lab setting. The system is comprised of three inertial measurement sensors, respectively attached and calibrated to the head, torso and hips, based on the subject's anatomical planes. Sensor output is transformed into meaningful clinical parameters of rotation (twist), flexion-extension and lateral bending of each body segment, with respect to calibrated global reference space. Modeling the spine as a compound flexible pole model allows dynamic measurement of three-dimensional spine motion, which can be animated and monitored in real-time using our interactive GUI. The accuracy of the proposed sensing system has been verified with subject trials using a VICON optical motion measurement system. Experimental results indicate an error of less than 3.1 degrees in segment orientation tracking.