Chromatin immunoprecipitation (ChIP) is a technique of choice for studying protein–DNA interactions. ChIP has been used for mapping the location of modified histones on DNA, often in relation to transcription or differentiation. Conventional ChIP protocols, however, require large number of cells, which limits the applicability of ChIP to rare cell samples. ChIP assays for small cell numbers (in the range of 10,000–100,000) have been recently reported; however, these remain lengthy. Our laboratory has elaborated fast ChIP assays suitable for small cell numbers (100–100,000) and for the immunoprecipitation of histone proteins or transcription factors under cross-linking conditions. We describe here a rapid micro (μ)ChIP assay suited for multiple parallel ChIPs from a single chromatin batch from 1,000 cells. The assay is also applicable to a single immunoprecipitation from 100 cells.