An object of the present invention is to provide a capillary electrophoresis apparatus in which simultaneity can be ensured between sensitivity and data acquisition to decrease a pull-up signal while spectral data acquisition is eliminated in each capillary exchange. The invention relates to a capillary electrophoresis apparatus in which capillary position shift is detected in each capillary exchange by detecting a capillary position. A capillary position measuring light source is provided in the capillary electrophoresis apparatus of the invention. The capillary is irradiated with light emitted from the capillary position measuring light source, a capillary image is detected with a two-dimensional detector, and thereby a position deviation of the capillary is determined. On the basis of the position deviation of the capillary, a data acquisition area is set in the two-dimensional detector, or a reference fluorescent light spectrum determined from the capillary at the standard position is corrected.