In this work, we address the optimal economical synthesis of an extractive distillation column for bioethanol purification, using ionic liquids as a type of solvent that can be designed to feature sustainable characteristics, such as low toxicity and low volatility, among other desirable properties. For the optimal synthesis of the separation scheme, we propose a mixed-integer nonlinear programming (MINLP) formulation, merged with disjunctive programming tools, to take care of modeling logical decisions [Yeomans and Grossmann, Ind. Eng. Chem. Res. 2000, 39, 1637-1648]. In a previous work [Chavez-Islas et al, submitted to Ind. Eng. Chem. Res.], we have addressed the design of a novel ionic liquid to separate the ethanol/water azeotropic system, up to high purities. The MINLP synthesis of the distillation column considers the feed tray location, the number of trays, and the operating and design parameters as decision variables. Because the ionic liquid used in this work is a novel solvent, its physical and thermodynamic properties are yet not available. Therefore, the physical properties of the ionic liquid are estimated using group contribution methods. The MINLP formulation is based on the application of the MESH equations for conditional trays, to reduce the size of the nonlinear subproblems and increase the robustness of the optimization formulation. The MINLP problem was solved using the SBB solver embedded in GAMS. Using the proposed MINLP formulation, we attained ethanol purities as good as 99.9 mol %, and 90% of the ethanol presented in the feed stream was recovered.