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In this paper, a novel technique is presented for accurately extracting the complex constitutive parameters (εˆ, μˆ) for individual layers of a multilayer sample using S-parameter waveguide measurements. The technique is based on a modified sequential quadratic programming algorithm, which utilizes a large number of initial guess points, thereby alleviating the possibility of local minima trapping. The algorithm was found to be significantly faster and more accurate than traditional global optimization methods such as the genetic algorithm. Computer-generated S-parameter data sets were initially used to establish the achievable accuracy of the algorithm for one-, two-, and three-layer cases. Sensitivity of the S-parameters to changes in the constitutive parameters and layer thicknesses was also investigated. Two-port S-parameter measurements (8.2-10 GHz) were conducted on three material samples in single and multilayer arrangements. The algorithm accurately extracted the complex constitutive parameters for each layer. These values were then compared with values extracted using a modified short-circuit line (SCL) method (single-layer cases only). S-parameters were also generated using the extracted values and compared with the measured data. In all cases, results were found to be in good overall agreement with both the SCL method values and the measured data.