An elongated or rectangular cross-section capillary is disclosed for use in capillary electrophoresis using optical detection. With rectangular capillaries, heat is efficiently dissipated which permits large volume applications in capillary electrophoresis. In addition, the increase in cell pathlength produces significant improvements in absorbance detection sensitivity. This advantage is also important for laser-induced fluorescence, optical rotation, and other pathlength-dependent detection schemes. Because flat walls produce less optical distortion than circular capillary walls, rectangular capillaries are particularly useful when parameters such as refractive index, photodeflection, direct visualization or particle counting are used for detection. Capillary electrophoresis employing rectangular capillaries allows for two-dimensional separations.