This paper addresses a systematic methodology for batch and semi-batch reactor design and optimisation for both ideal and non-ideal mixing. It can be applied to non-isothermal and multiphase systems. The method starts from a general representation in the form of a temporal superstructure based on the similarity of between plug flow reactors and ideal batch reactors. The temporal superstructure of a batch reactor exists in both the space and time dimensions. For non-ideal mixing, this paper addresses a mixing compartment network model to represent mixing inside reactors. The mixing compartment network is then included into the temporal superstructure to model non-ideally mixed batch reactors and the mixing pattern optimised with the other variables. Besides the operation variables for batch reactors, this method can also suggest the optimum mixing pattern and promising reactor configurations for mechanical design. A profile-based approach is proposed to make a search of the profiles for temperature, pressure and feed addition. This approach starts from a set of initial profiles of temperature, pressure and feed addition. Then the performance of the batch reactor is evaluated against the objective function under different profiles. An optimal set of profiles is then found by this profile searching process. A stochastic optimisation technique based on simulated annealing is employed to obtain optimal solutions. This method is also extended to multiphase reaction systems based on the concept of shadow reactor compartments. A number of case studies are presented to illustrate the use of the proposed methodology. (C) 2003 Elsevier Ltd. All rights reserved.