Chromatin immunoprecipitation (ChIP) is a powerful method for mapping protein-DNA interactions in vivo. Genomic localization of histone modifications, transcription factors, and other regulatory proteins can be revealed by ChIP. However, conventional ChIP protocols require the use of large numbers of cells, which prevents the application of ChIP to rare cell types. We have developed ChIP assays suited for the immunoprecipitation of histone proteins or transcription factors from small cell numbers. Here we describe a rapid, yet sensitive micro (μ)ChIP protocol producing high signal to noise ratio output, suitable for as few as 100 cells. This chapter provides a detailed protocol for μChIP from early mammalian embryos, also suitable for any sample of limited numbers of cells. Minor modifications of this optimized high signal to noise ChIP protocol make it a reliable tool for the use with any cell number (100-10(7)).