Polygeneration, a multi-input multioutput energy conversion process which typically involves the coproduction of electricity and liquid synthetic fuels, is a promising technology which offers real potential toward the reduction of excessive energy consumption and consequent greenhouse gas emissions. The optimal design of such a complex and nonlinear process system under inevitable and unpredictable future uncertainty poses great challenges in terms of both modeling and corresponding solution strategies. In this paper, we propose a stochastic programming framework for the optimal design under uncertainty of polygeneration energy systems. On the basis of a detailed mixed-integer nonlinear programming (MINLP) model, proposed in our previous work, a two-stage stochastic programming problem is formulated, which is then converted into a large-scale multiperiod MINLP problem by employing cubature based integration and sampling techniques. A decomposition algorithm is utilized for the efficient solution of the multiperiod problem, which involves iterations between a set of nonlinear subproblems of much smaller size and a master mixed-integer linear programming problem. A case study is then presented, where detailed computational results and comparisons between optimal designs obtained for both the stochastic and deterministic cases are shown.