Analysis of a nucleic acid samples having thousands of bases is conducted by capillary electrophoresis. The electrophoretic section is provided with a first capillary filled with an agarose gel and a second capillary filled with a polyacrylamide gel. An on-column detector is incorporated with the second capillary for optical detection. To fill a capillary with a gel, a solution is fed under high pressure from a first flow channel through a switching valve into a second flow channel connected to the capillary. To inject a sample in the capillary, a sample injector is connected to a switching valve passage, and a buffer solution is connected to the capillary through a flow channel and the switching valve. After switching the valve, the first passage is incorporated into the flow channel between the buffer solution and the capillary being filled. Then, the sample is electro-kinetically injected into the capillary. When conducting genetic polymorphism by electrophoresis, temperature control elements are provided to maintain the capillary at a predetermined temperature and a DNA sample device is provided to heat the sample to a temperature higher than a disassociation temperature thereof for directly injecting the heated sample into the capillary.