A formulation is presented for the optimal selection of both the equipment units and the network of connections for multipurpose batch plants so as to satisfy given production requirements for a variety of products. The model includes very general constraints and objective functions and permits to optimize simultaneously the structural aspects of the plant and the associated production schedule, accounting for both capital costs of equipment units and pipework, operating costs and revenues. A special novelty of the formulation is that it provides the possibility of generating directly the optimal connectivity between the process units, optimal sizing and costs of the transfer lines, and the optimal storage policies (and associated vessel sizes, if any) for stable intermediates without the need for a priori assumptions (e.g. unlimited storage, etc.). The resulting MILP problem is solved using a branch and bound method. Several examples are detailed, demonstrating the generality of the approach and the importance of including structural and operational aspects at the design stage. The flexibility of the formulation permits utilizing various design strategies, from a simultaneous optimization of all problem decisions (equipment, connections and schedule) to a sequential optimization of main equipment, followed by the design of connections etc. These strategies are also illustrated by an example.