Histone deacetylases are important regulators of transcription and an emerging target for anticancer drugs. We present an overview over various assay formats that include radiolabelled histones, oligopeptides, and small molecules as substrates. The advantages and disadvantages of the various formats in terms of, e.g., substrate availability, throughput or subtype selectivity are discussed. Detailed procedures for various assay types that can be used for different problems, such as library screening or fluorescent inhibitor testing, are given. We present a new protocol for a simple high-throughput assay for NAD+-dependent (class III) histone deacetylases, also termed sirtuins.