Nearly all signal transduction pathways lead to regulation of gene expression by controlling specific transcription factors (TFs). Chromatin immunoprecipitation (ChIP) is a powerful method for studying TF-DNA interactions in vivo. To identify all binding sites of a TF in the genome, the DNA obtained in ChIP experiments needs to be analyzed by hybridization to genome-tiling microarrays (ChIP-chip) or by next-generation sequencing (ChIP-seq). Here, we provide detailed protocols of ChIP for two model plant species Arabidopsis and rice, procedures of DNA sample preparation for ChIP-chip or ChIP-seq, and a general guide for computational data analysis. We have used these protocols to successfully identify direct target genes of the BZR1 TF of the brassinosteroid signaling pathway in both Arabidopsis and rice.