This paper presents a method for analyzing the complete behavior of industrial robotic manipulators with complex-shape flexible links, including the effects of the manipulator’s control systems and actuators. The kinematics and dynamics of the manipulator are expressed in terms of 4 × 4 matrices. The distributed flexibility and mass properties of the links are obtained by using readily available finite-element models and programs. The resulting equations are transformed to produce a method which is computationally efficient through a procedure called Component Mode Synthesis. The method is applied to an actual industrial manipulator and the results are compared to experimental data, showing good correlation. Link flexibility is demonstrated to have significant impact on system performance and stability.