The paper describes the control and friction compensation of a robot with flexible joints (the DLR medical robot), which has strong mechanical couplings within pairs of joints realized with a differential gear-box. In consideration of this coupling, a MIMO state controller is designed for the strongly coupled joints. In addition a disturbance observer is developed to compensate the nonlinear effects of the friction and to improve the position accuracy of the robot. It is shown that the system is global asymptotically stable for the MIMO controller and the disturbance observer. Finally, experimental results with the DLR medical robot are presented validating the proposed concept.