Protein–DNA interactions play crucial roles in various biological processes, such as transcriptional regulation, histone modifications, DNA damage repair, and cell cycle progression. Chromatin immunoprecipitation (ChIP) is a powerful technique used to study interactions between proteins and DNA within cells. This technique has not only clarified the relationships among transcription factors, histone modifications, and gene regulation but also facilitated extensive genome-wide analyses of protein-DNA interactions. In this chapter, we provide a detailed overview of the ChIP-quantitative PCR (qPCR) technique, emphasizing its application in investigating the interactions between viral genomes and host proteins through ChIP-qPCR analysis.