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Multidisciplinary design optimization based on independent subspaces (MDOIS) is a simple and practical method that can be applied to the practical engineering MDO problems. However, the current version of MDOIS does not handle the common design variables. A new version of MDOIS is proposed and named as MDOIS/2006. It is a two-level MDO method while the original MDOIS is a single-level method. At first, system analysis is performed to solve the coupling in the analysis. If the termination criteria are not satisfied, each discipline solves its own design problem. Each discipline in the lower level solves the problem with common design variables while they are constrained by equality constraints. In the upper level, the common design variables of related disciplines are determined by using the optimum sensitivity of the objective function. To validate MDOIS/2006, mathematical problem and NASA test bed problem are solved. The results are compared with those from other MDO methods. Finally, MDOIS/2006 is applied to flow patterner design and shows that it can be successfully applied to the practical engineering MDO problem.