Imprinted genes are marked by parental allele speci fi c DNA methylation and histone modi fi cations which regulate their monoallelic expression. Chromatin immunoprecipitation (ChIP) is the technique of choice to characterize the histones associated with either maternal or paternal chromosomes. To study allelespeci fi c chromatin composition at imprinted regions, the method has to be ef fi cient to work on limiting amount of starting material, and speci fi c enough to recognize one of the parental alleles. We optimized the commonly used ChIP technique for ef fi cient recovery of one parental allele from small number of cells. We provide examples to show that this ChIP protocol can speci fi cally distinguish between parental alleles in mouse embryo fi broblasts carrying maternal and paternal duplication of mouse distal Chr7 and also in normal mouse embryo fi broblasts carrying single nucleotide polymorphism at imprinted regions.