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In this paper, a novel actuation system for Wireless Capsule Endoscopes (WCE) based on magnetic levitation is proposed. This study focuses on the design of a multi-input, multi-output (MIMO), controller to maintain a desired position and orientation of the capsule relative to the movable electromagnet frame so that it can navigate the intestine by moving this frame and/or the patient. Tracking algorithms for the linear controller based on pole placement, entire eigenstructure assignment (EEA), and linear quadratic regulator (LQR) techniques are designed and simulated using Matlab/Simulink. Simulation results suggest that the LQR controller can be used for capsule actuation.