Capillary electrophoresis (CE) and immunosubtraction capillary electrophoresis (IS-CE) were compared with the conventional methods agarose gel electrophoresis (AGE) and immunofixation electrophoresis (IFE) for detection and identification of paraproteins. In total, 74 paraproteins out of 468 serum samples were detected by both methods. Seventy-three monoclonal bands with concentrations ranging from 0.6 to 50.9 g/L were detected by the routine method. With CE, 70 paraproteins were detected and quantified on the electropherogram. Four paraproteins were not detected by CE; three of these were IgG (0.6, 1.1, and 2.2 g/L, respectively), and one was a IgM paraprotein (20.3 g/L) that could be visualized by minor changes in the running conditions. In comparison with IFE, 69 paraproteins were typed identically using IS-CE; only one paraprotein (IgMκ, 14.9 g/L) could not be identified. On the other hand, a monoclonal IgA band that had not been detected by AGE was identified by CE and IS-CE. We conclude that, in general, CE could be a useful method for detection of paraproteins and that IS-CE is a good alternative to IFE. Additional studies are required to investigate the ionic strength and pH of the running buffer, because these prove to be the most crucial factors for routine CE separation of paraproteins.