The present invention concerns a device and a method for filtering molecules that is precise, efficient, reliable, and rapid; it has a low rate of molecular loss, it can be upgraded, and it provides for the automated filtration of molecules according to one or more predefined parameters. The device (10) for filtration of molecules (3) comprises three filtration zones (11a-11c), each equipped with filtration reservoirs (1) in which a solution containing molecules (3) to be filtered is placed. The filtration reservoirs (1) are separated into two chambers by an isoelectric filter (4) which allows only selective passage of molecules (3) according to their isoelectric point (pI) when they are subjected to an electrical field generated by electrodes (5). This filtration device (10) comprises a mechanized tool holder (20) specifically for supporting one or more pairs of electrodes (5) in order to perform isoelectric filtration in one or more filtration reservoirs (1) simultaneously.