A generalized disjunctive programming formulation is presented for the optimal design of reactive distillation columns using tray-by-tray, phase equilibrium and kinetic based models. The proposed formulation uses disjunctions for conditional trays to apply the MESH and reaction kinetics equations for only the selected trays in order to reduce the size of the nonlinear programming subproblems. Solution of the model yields the optimal feed tray locations, number of trays, reaction zones, and operating and design parameters. The disjunctive program is solved using a logic-based outer-approximation algorithm where the MILP master problem is based on the big-M formulation of disjunctions, and where a special initialization scheme is used to reduce the number of initial NLP subproblems that need to be solved. Two examples are presented that include reactive distillation for the metathesis reaction of 2-pentene and for the production of ethylene glycol. The results show that the proposed method can effectively handle these difficult nonlinear optimization problems.