As an effective method of studying soluble protein-protein interactions, yeast display system is now widely used for affinity maturation of single-chain antibodies. Due to the strong homology recombination machinery of yeast and the high-throughput nature of FACS detection, a rapid scan for interaction between antigen-antibody pairs could be easily achieved. Based on this system, a novel and reliable method for determining conformational epitopes was developed. Different fragments of macrophage migration inhibitory factor (MIF) and several point mutations of MIF were displayed on yeast cell surface using homologous recombination technology. Three MIF monoclonal antibodies, 10C3, 2A12 and 4E10, were screened for their binding affinity to each displayed peptide. Utilizing this technology, the key amino acids of MIF that bind to the MIF monoclonal antibodies were easily identified.