Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful technique for genome-wide profiling of DNA-binding proteins in vivo. ChIP has been used to study diverse nuclear processes such as transcription regulation, at specific loci as well as across the entire genome. In this report, a protocol is described for the application of ChIP to the genome-wide analysis of the distribution of different RNA polymerase II forms. The method makes use of the possibility to crosslink proteins to the DNA, to which they bind in vivo. Specific RNA-Pol II-DNA complexes can then be purified by immunoprecipitation using a specific antibody against the DNA-binding protein of interest, and the associated DNA fragments recovered and analyzed.