Chromatin immunoprecipitation (ChIP) is widely used in many fields to analyze the distribution of specific proteins, or their modified isoforms, across defined DNA domains. ChIP procedures fall into two main categories, namely, those that use native chromatin prepared by nuclease digestion (designated NChIP), and those that use chromatin in which DNA and proteins are crosslinked, either chemically or with UV light (designated XChIP). Each procedure has its own advantages and drawbacks. Here, we outline the methods currently in use in our laboratory to isolate and immunoprecipitate native chromatin from cultured cells, and to isolate and analyze immunoprecipitated protein and DNA.