Motion analysis is increasingly used to study the complex kinematics of the musculoskeletal system. In this chapter, both the theory and applications of motion analysis are presented. After the definition of a Cartesian coordinate frame is introduced, a description of transformations between multiple coordinate frames is given; the decomposition of a transformation matrix into anatomical joint motion parameters (e.g. Euler angles) is then explained. Kinematic analysis in musculoskeletal research is illustrated by several examples. The first example describes a reaching-and-grasping task in which mathematical transformations are applied to position the hand with respect to an object during grasping. The second example demonstrates the utility of motion analysis in revealing the coupling motion of the wrist between flexion-extension and radial-ulnar deviation. The third example shows the application of the motion analysis technique to the study of thumb kinematics, providing insight into the complex movements of thumb joints generated by individual muscles. The last example illustrates the study of knee biomechanics, including a description of knee joint kinematics during functional activities and determination of in situ ligament forces using robotic technology. It is hoped that the theoretical knowledge and biomechanical examples will help readers apply the motion analysis technique to various research problems associated with the musculoskeletal system.