A systematic procedure is proposed for designing an internally heat integrated distillation column which separates a binary mixture. In the proposed procedure, the liquid compositions in the column are discretized and each of them is assigned to a stage in a column. The feature of the proposed procedure is that the structure of vapor and liquid paths among the stages are treated as design variables. The combinations of the heat exchange stages in the stripping and rectifying sections are also treated as design variables. As the liquid composition of each stage has been decided in advance, the state variables related to each stage can be calculated before solving the synthesis problem. Thus, the design problem is formulated as a mixed integer linear programming problem, and the optimal column structure is derived by solving it. The proposed method was applied to the problems of separating a benzene-toluene mixture. The results show that the structure of an internally heat-integrated distillation column is systematically derived. Furthermore, an unexpected innovative structure called a stepwise condenser was generated by the proposed procedure.