An electrophoresis method, system, and gel recover biological substances from the gel with high efficiency. The method uses an electrophoresis gel having an injection hole into which biological substances are injected and a recovery hole from which the biological substances are recovered. The electrophoresis method includes injecting the biological substances into the injection hole, and applying an electric field penetrating the injection and recovery holes. A vertical axis in a downward direction as a positive direction is set as an X-axis, an axis which is perpendicular to the X-axis is set as a Y-axis, and coordinates of a bottom of the recovery hole are set as (XC, YC). The X coordinate XC of the bottom of the recovery hole satisfies XC>X1 when the biological substance is electrophoresed to coordinates (X1, YC) in the recovery hole from a bottom of the injection hole in the applying the electric field.