In this paper we describe the use of high performance liquid chromatography (HPLC) and capillary electrophoresis (CE) as rapid and automated techniques for the analysis of DNA fragments generated by the polymerase chain reaction. Unlike traditional slab gel electrophoresis, these techniques allow a single-step qualitative and quantitative analysis of DNA. Furthermore, both techniques allow the detection of DNA fragments with high sensitivity in the subnanogram to microgram range. The complete automation of the instrumentation permit the unattended analysis of a great number of samples, and the direct entry of the data into a computer facilitates the processing of large numbers of PCR products. Furthermore, the HPLC technique allows the recovery with quantitative yield of pure DNA fragments suitable for other applications.