Specific combinations of post-translational modifications of histones alter chromatin structure, facilitating gene transcription or silencing. Here we have investigated the 'histone code' associated with the histone methyltransferases Suv39h1 and G9a by combining double immunopurification and mass spectrometry. Our results confirm the previously reported histone modifications associated with Suv39h1 and G9a. Moreover, this method allowed us to demonstrate for the first time an association of acetylated histones with the repressor proteins Suv39h1 and G9a.