ChIP-seq is rapidly becoming a routine technique for the determination of the genome wide association of DNA binding proteins and histone modifications. Here we provide a protocol for the isolation, purification, and immunoprecipitation of DNA fragments associated with a target transcription factor of interest. Although the method makes use of adult mouse hearts, it can, with relative ease, be adapted for the in vivo ChIP isolation of DNA from other cell and tissue sources with the intention of massive parallel sequencing.