We have developed a gel electrophoretic approach for visualizing and cloning protein binding sites from complete genomes. This system consists of a simple two‐dimensional band shift, in which protein‐DNA complexes are retarded in the first dimension, performed at low temperature, and disrupted in the second dimesion, performed at high temperature. We present here results obtained with the integration host factor (IHF) and cAMP receptor protein (CRP) proteins of Escherichia coli, and discuss some of the important methodological aspects of the technique.