Applying a genetic algorithm for the optimization of trace element composition in the medium for L-isoleucine production from glucose and DL-alpha-hydroxybutyric acid with Corynebacterium glutamicum resulted in a reduction of the byproduct L-valine. High L-isoleucine broth concentrations of 20 g/l within 72 h at an L-isoleucine/DL-alpha-hydroxy butyric acid yield of 70% (w/w) and an L-isoleucine/L-valine ratio of 100 were achieved, if closed-loop control of glucose and of DL-alpha-hydroxybutyric acid was applied. For the isolation of L-isoleucine from fermentation broth a specific downstream processing was developed and optimized up to semitechnical scale (ultrafiltration, reverse osmosis, first crystallization, active-carbon adsorption, electrodialysis, second crystallization). The economic model of this downstream processing, which was identified by coupling the mass balance and energy balance with the semi-empirical models of the unit operations, was used to quantify the isolation costs as a function of L-isoleucine concentration and L-isoleucine/L-valine ratio in the fermentation broth. A cost reduction for downstream processing from DM 55 to DM 25 (kg L-isoleucine)(-1) and an improvement of the L-isoleucine yield in downstream processing from 48% to 80% was achieved using this economic model as the objective function to be minimized by the fermentation process (scenario : production of 70 tonnes L-isoleucine/year).