In a capillary electrophoresis apparatus, a capillary array unit has a capillary array including capillaries having a capillary head and a detection unit, a frame for supporting the capillary array, and a load header for holding cathode ends of the capillaries. The frame has separators for separating and holding the capillaries. The capillary head, the detection unit, and the separators are disposed along one linear line. With this arrangement, there is provided the capillary array unit and the capillary electrophoresis apparatus which are arranged such that a job for mounting the capillary array can be executed easily.