Routine DNA analysis is assuming an increasing importance in clinical medicine as well as in basic research. The expanding field of DNA diagnostics will take advantage of the growing understanding of the molecular basis of human disease. Similarly, extensive studies of the structure of large genomes require efficient analytical techniques. In this chapter a strategy will be described that permits rapid distinction between alternate DNA sequences under standardized conditions. Applications of the technique includes screening for mutant gene sequences and genetic linkage analysis. The analysis may be performed manually or by a laboratory workstation resulting in a generally applicable automated gene analysis technique.