Eukaryotic DNA is wrapped around histone octamers, known as nucleosomes, in an orderly fashion that provides the primary structure of chromatin organization. The compaction of DNA into nucleosomal repeats not only allows the tight packaging of the large eukaryotic genomes into the nucleus, it also dictates the accessibility of genetic information. Thus, in order to understand how nucleosomes can affect the dynamics of DNA–protein interactions, such as those associated with transcriptional regulatory mechanisms, it is important to define nucleosomal positioning and occupancy along genomic DNA. Here we describe a method that relies on the enzymatic activity of micrococcal nuclease (MNase) to determine nucleosomal footprints and boundaries. By pairing this technique with next generation sequencing techniques (i.e., MNase-seq), it is possible to generate a genome-wide detailed map of chromatin architecture.