Covalent modifications on the nucleosomal histones are essential in chromatin regulation and gene expression. Patterns of histone modifications may be somatically maintained and can thereby maintain locus-specific repression/activity in defined lineages or throughout development. During recent years, histone acetylation and methylation have emerged as key players in the repression or activation of genes and chromosomal domains. Histone methylation and acetylation patterns (and other histone modifications) can be analyzed by chromatin immunoprecipitation (ChIP). This chapter describes how ChIP can be performed on native chromatin prepared from cells and tissues, in order to analyze histone methylation and acetylation at specific sites in the genome. We also present different PCR-based assays that can be applied to analyze loci of interest in immunoprecipitated chromatin fractions.