A microscale normal flow filtration (NFF) technique has been established for the automated high throughput evaluation of complex biological feed streams. A commercially available 96-well filter plate (0.3 cm(2) per well) and a custom designed 8-24-well filter plate (0.8 cm(2) per well) were used to quantitatively study the microfiltration characteristics of an Escherichia coli TOP10 fermentation broth. Microwell results, from up to 96 independent experiments, were obtained in parallel using an automated vacuum filtration manifold. These were verified against a conventional laboratory scale membrane cell (3.8 cm(2)). All formats used a 0.22 mu m Durapore PVDF membrane and initial water flux experiments showed measured membrane resistances to be equivalent and of the order of 5 x 10(10) m(-1). Specific cake resistances of E. coli TOP10 cells under various filtration conditions were next determined using both filter plate designs and shown to be equivalent to those determined using the membrane cell. Up to three-fold differences in specific cake resistances were found in experiments examining the effect of fermentation broth harvest time on microfiltration performance and the presence of specific buffers (100 mM acetate) or media components (10gL(-1) yeast extract) in the feed stream. Compared to commercial multi-well filter plates the custom designed plate reduces the errors associated with microscale experimentation and also allows simultaneous evaluation of different membrane types. Used alongside microwell fermentation studies the technique presented here allows for the integrated optimisation of upstream and downstream operations. (c) 2005 Elsevier B.V. All rights reserved.