BACKGROUND: The performance of three particle swarm optimisation (PSO) algorithms was assessed in relation to their capability to optimise an alternative fermentation process for the production of biobutanol. The process consists of three interconnected units: fermentor, cell retention system and vacuum flash vessel (responsible for the continuous recovery of butanol from the broth). The dynamic behaviour of the process was described by a non-linear mathematical model. Four constrained optimisation problems were formulated concerning the operation and design of flash fermentation: (1) maximisation of butanol productivity; (2) maximisation of substrate conversion; (3) and (4) adjustment of operating conditions in the face of problems of fluctuations in the quality of the agricultural raw material and changes in the kinetics of the microorganisms.