This chapter reports an overview of the analytical techniques used to perform genetic analysis of polymerase chain reaction products using capillary electrophoresis. Three separate but related techniques are described: the separation of native DNA with detection using fluorescent intercalating dyes, the separation of denatured DNA using fluorescently labeled primers, and the detection of single-strand conformation polymorphisms using denatured DNA separated under native conditions. The various techniques involve electrokinetic injection of the DNA onto a narrow band at the head of the column, sieving the DNA through various entangled polymer matrices, and detection via single or multichannel laser-induced fluorescence. Analytical protocols are provided, and a series of representative electropherograms are included.