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Chromatin immunoprecipitation (ChIP) maps, on a genome-wide scale, transcription factor binding sites, and the distribution of other chromatin-associated proteins and their modifications. As such, it provides valuable insights into mechanisms of gene regulation. However, successful ChIP experiments are dependent on the availability of a high-quality antibody against the target of interest. Using antibodies with poor sensitivity and specificity can yield misleading results. This can be partly circumvented by using epitope-tagged systems (e.g., HA, Myc, His), but these approaches are still antibody-dependent. HaloTag® is a modified dehalogenase enzyme, which covalently binds synthetic ligands. This system can be used for imaging and purification of HaloTag® fusion proteins, and has been used for ChIP in vitro. Here, we present a protocol for using the HaloTag® system for ChIP in vivo, to map, with sensitivity and specificity, the cistrome of a dynamic mouse transcription factor expressed at its endogenous locus.Graphical abstract: