An electrophoretic method for separating large DNA molecules which uses periodically inverted electric fields of different magnitude in the two directions is described. Net DNA migration is either in the high field direction or in the low field direction, depending on the relative duration of the pulses. With this approach, molecules of up to 1.6 million base pairs can be separated in parallel lanes after a single run under fixed timing conditions. An inexpensive switching unit is the only device needed in addition to the conventional gel box.