This article describes a fully automated system for the on-line monitoring and closed-loop control of a fed-batch fermentation of recombinant Escherichia coli, and presents two case studies of its used in limiting production of unwanted byproducts such as acetic acid in fed-batch fermentations. The system had two components. The first component, on-line monitoring, comprised an aseptic sampling device, a microcentrifuge, and HPLC system. These instruments removed a sample from a fermentor, spun it at high speed to separate solid and liquid components, and then automatically injected the supernatant onto an HPLC column for analysis. The second component consisted of control algorithms programmed using the LabView visual programming environment in a control computer that was linked via a remote control unit to a feed pump. The monitoring and control components were linked so that the results from the on-line HPLC were captured and used by the control computer in real time. In one of the case studies, the control algorithm was designed to demonstrate coarse feedback control to confirm the operability of the controller. The second case study showed how the system could be used in a more sophisticated feeding strategy providing fine control and limiting acetate concentration to a low level throughout the fermentation.