A capillary electrophoresis system comprising a plurality of capillaries filled with a migration medium in which samples to which fluorephore labels are added migrate, a light source providing an excitation light exciting the fluorephore labels, a photo detector detecting a fluorescence radiated from the fluorephore labels, and light focusing means placed between the plurality of capillaries to which the excitation light is irradiated. The parts of the plurality of capillaries to which the excitation light is irradiated and the light focusing means are arranged in a plane shape. The excitation light is irradiated through the plurality of capillaries and the light focusing means, the capillaries and light focusing means alternatively placed in the parts where an excitation light is irradiated. The light focusing means consisting of cylindrical rod lenses. The axis of the cylindrical rod lenses is placed substantially parallel with the capillaries, which can detect the fluorescence from samples by irradiating a plurality of capillaries substantially at the same time in a batch without mechanical scanning of a plurality of capillaries or without optical scanning of a light beam, providing a highly sensitive detection of samples.