Capillary array instrument was applied to transcript profiling of the yeast genomic DNA using GeneCalling(TM) chemistry. The instrument integrated a 12-capillary array for DNA separation with a replaceable sieving matrix, laser-induced fluorescence detection and an automated microfraction collector. The DNA fractions, exiting the separation capillaries, were continuously deposited in a 1536-well collection plate made of agarose gel. DNA fragments recovered from selected fractions were cloned and then sequenced. Over 80% of theoretically predicted fragments could be recovered in the collected fractions, cloned and sequenced with an average redundancy of threefold. Excellent correlation of the experimentally obtained sequences with the theoretically predicted gene fragments demonstrated the suitability of capillary array electrophoresis for micropreparative recovery of DNA fragments. This approach, useful especially for rapid DNA expression profiling of unknown genes for nonsequenced organisms, demonstrates the practical capability of the prototype multicapillary fraction collector.