The movement characteristics of flagellated microorganisms were investigated using a novel microscope-based online imaging tool for fermentation control. A flexible flow through cuvette run in a chopped mode was used. The cuvette allows observations of microorganisms in a depth of field of 3 mu m. The whole process of sampling, image acquisition and analysis is fully automated. Besides the measurement of the velocity of flagellated microorganisms, in this study the ability of the system to measure characteristic movement patterns of the bacteria is described for the first time. This information allows further conclusions on the viability status of bacteria during fermentation processes and can be used for fermentation optimization.