The invention relates to a method and apparatus for carrier-free deflection electrophoresis, in which a separating media and a sample to be examined flow through a separating chamber between a pair of electrodes in a series of reversing bulk fluid flow along the direction of the electrodes, thereby separating the sample into zones which are to be collected into fractions for analysis or further processing. Among other things, the apparatus and method enable high-resolution separation of particles that can be performed in miniaturized chambers in electrophoresis modes including isoelectric focusing, zone electrophoresis, and isotachophoresis.