The capillary electrophoresis apparatus according to the present invention can maintain the temperature in the longitudinal direction of each of a plurality of capillaries uniformly, such that the separation performance of the capillary electrophoresis apparatus can be stabilized, and the analysis performance can be improved. A capillary electrophoresis apparatus according to the present invention includes: a thermostat having a heat source, a first heat conduction member, and a detection window for detecting a sample, the thermostat being configured to maintain a capillary at a predetermined temperature; a capillary holder having a second heat conduction member for sandwiching the capillary between the second heat conduction member and the first heat conduction member, the capillary holder being configured to hold the capillary; and a detection unit configured to detect a sample to be electrophoresed in the capillary, wherein in the heat source, a heat generation amount of at least one of a periphery of the detection window and an end of the capillary is higher than a heat generation amount of another portion.