To attempt to gain an understanding of the molecular underpinnings of disease, many researchers have turned to expression profiling of genes during various stages of host recognition, entry, invasive growth, and host responses. While these studies have proven valuable, a deeper level of knowledge of the control circuitry affecting observed gene expression profiles can lead to a better understanding of the host pathogen interaction. Transcription factors are key switches in signal transduction circuits regulating gene expression. One powerful method to define target sequence specificity for this important group of transcription regulators is chromatin immunoprecipitation (ChIP) with microarray chips (chip), commonly called ChIP-chip. A more recent variation of this technique is ChIP-seq where DNA sequencing replaces the microarray chip. Here, we describe how we elucidated the binding sites for the Magnaporthe oryzae Ca(2+)/calcineurin-dependent transcription factor MoCRZ1 with the ChIP-chip approach.