Understanding the binding of regulatory proteins to their cognate genomic sites is an important step in deciphering transcriptional networks such as the circadian oscillator. Chromatin immunoprecipitation (ChIP) enables the detection and temporal analysis of such binding events in vivo. Here, we describe the individual steps from the generation of formaldehyde-cross-linked chromatin from mouse liver nuclei, fragmentation thereof, immunoprecipitation, reversal of cross-links, fragment cleanup, and detection of binding sites by real-time PCR. Depending on the quality of the employed antibody, a clear enrichment signal over the background is expected with a resolution of about 500–800 base pairs around the selected primer–probe pair.