Fluorescent-labeled microspheres (FM) are a new tool for the determination of organ blood flow. However, the FM-method is labor intensive, because of the necessity to recover the microspheres from the tissue samples. The aim of this study was to automate the FM-method. A Zymate-Robotic System (Zymark, Idstein, Germany) was modified to handle a novel filtration device. The robot is surrounded by 12 different stations which are necessary to process the samples. It performs the sequential steps which are needed to recover the microspheres from the samples. The dyes are finally released from the FM with a solvent and their fluorescent intensity is measured online using a spectrophotometer (Perkin Elmer, Uberlingen, Germany). The robotic system is able to recover the FM through digestion and filtration of the tissue samples using the new filter, to dissolve the FM and to release the dyes so that their fluorescent intensities can be measured for the calculation of organ blood flow.