This paper presents a systematic methodology for designing adaptive feedback linearization controller for high purity binary distillation column having uncertain parameters and input saturation. Main goal of the controller is to control the top and bottom compositions of a binary distillation column in presence of both structured and unstructured uncertainty. An adaptive control strategy is used for the estimating uncertain parameters in the system model. Process input saturation always causes an added nonlinearity to the process, leading the process to become uncontrollable. A cascade reduced order nonlinear adaptive controller is designed and implemented to handle both forms of structured and unstructured uncertainty and input saturation problem. (C) 2008 Elsevier Ltd. All rights reserved.