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In this paper, a new synthesis and design methodology is presented and applied for the fast and accurate design of inductive rectangular waveguide filters. By using this technique, the dimensions of both homogeneous and inhomogeneous filters can be successfully synthesized for almost any practical filter bandwidth, return loss, or filter order. This novel technique is based on a prototype with additional degrees of freedom, able to match the response of the different filter components in a wideband frequency range, and an elaborated design procedure that fully exploits this flexibility. During the design procedure, the prototype and the real structure are continuously aligned in order to have the same electromagnetic behavior and jointly evolve to obtain an equiripple response. Once the final prototype has been synthesized, excellent filter dimensions can be extracted that, in most cases, do not require further optimization. Examples will show the outstanding performance of the proposed design technique in terms of versatility, accuracy, and CPU time.