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This paper presents an efficient and well structured design methodology for designing complex FPGA (Field Programmable Gate Array) based controllers. To illustrate the interest and the particularity of this methodology, a complex sensorless control algorithm for a synchronous machine has been chosen. This algorithm consists of an Extended Kalman Filter (EKF) which is used to estimate rotor position and speed. In this paper, the whole design methodology steps are discussed. For the developed application, a preliminary system specification is made. Then, the algorithm development and the FPGA-based architecture development are separately presented. Finally the experimental validation is presented.