Histone deacetylase 4 (HDAC4) is a histone deacetylase profoundly involved in cell differentiation and in the pathogenesis of cancer. The histone deacetylase inhibitors are a new, promising class of anticancer agents. The screening of molecular interactions involving determination of the affinity of drug candidates is an integral part of the drug discovery process. Here we report the development of an assay using surface plasmon resonance for the analysis of HDAC4-small molecule interactions. We describe a new cloning and purification strategy that can be used to set up surface plasmon resonance experiments with other recombinant proteins.