Bacterial adaptation to given environmental conditions is largely achieved by complex gene regulatory processes. To address the question how and to what extend single transcriptional regulators modulate gene expression, chromatin immunoprecipitation (ChIP) coupled to DNA microarrays (ChIP-chip) or to next-generation sequencing (ChIP-seq) is one of the preferred methods. Both ChIP-chip and ChIP-seq can generate genome-wide maps of protein-DNA interactions and thus identify primary regulons of transcription factors. In combination with transcriptome analyses, the obtained data can be used to compile complex regulatory networks which in terms will advance our understanding of bacterial adaptation processes to specific environmental conditions.