Organisms exhibit daily changes of physiology and behavior to exert homeostatic adaptations to day-night cycles. The cyclic fluctuation also takes place at transcriptional levels, giving rise to rhythmic gene expression. Central to this oscillatory transcription is the core clock machinery which constitutes a circuit of transcriptional-translational feedback and achieves circadian functions accordingly. Chromatin immunoprecipitation provides understanding of such mechanisms that clock and non-clock transcription factors along with co-regulators and chromatin modifications dictate circadian epigenome through cyclic alterations of chromatin structures and molecular functions in a concerted fashion. Besides, innovation of high-throughput sequencing technology has broadened our horizon and renewed perspectives in circadian research. This article summarizes the methodology of a chromatin immunoprecipitation experiment in light of circadian rhythm research.