The present invention provides a capillary electrophoresis apparatus in which a capillary is easily attached to and detached from a migration medium filling unit without mixing impurities into the capillary. Mixture of impurities such as dust is also prevented when a capillary negative-electrode end is brought into contact with a sample stored in a vessel. Furthermore, temperature control is efficiently performed in the capillary. In the capillary electrophoresis apparatus, the whole of capillary array can be supported by grasping a grip portion by hand. A migration medium filling mechanism includes a slide mechanism which moves a polymer block with respect to a capillary head. The capillary electrophoresis apparatus includes a vessel in which a sample and a buffer can simultaneously be stored. Temperatures of the capillary and an irradiation and detection unit are controlled by a temperature control function provided in a thermostatic device.