The use of an automated multiwell method for assessing the normal flow filtration of purified DNA solutions containing plasmids and bacterial artificial chromosomes is presented. The custom multiwell filter design (filtration area of 0.28 cm(2) per well) allowed the use of low DNA volumes and that experimental replicates be performed simultaneously with parallel analysis of multiple parameters. Using the multiwell system, the behaviour of purified DNA solutions was studied when operating pressure, vectors size and membrane type was varied. Operating pressures of 30-65 kPa were applied and showed little effect on membrane capacity. Flux and membrane capacity decreased significantly with increasing vector size (6-72 kb). Filtration using different 0.2- or 0.22-mu m rated polyvinylidene difluoride and polyethersulfone membranes were evaluated and the results showed difference in flux and transmission rates. Results were verified against conventional membrane filter capsules with larger filtration areas of 0.65 and 3.9 cm(2). Information on filter capacity was comparable between the multiwell and conventional systems. This is particularly useful at the early stages of product development where only limited amounts of material are available. By conducting the experiments on a robotic platform, automated liquid sensing, continuous feeding and integration of analysis techniques were enabled. (C) 2010 Elsevier B.V. All rights reserved.