Disulfide bond formation in the refolding of thermophilic fungal protein disulfide isomerase (PDI) was investigated. It was revealed that (i) a disulfide bond buried inside the molecule is preferentially formed and contributes to the thermal stability and the isomerizing power of PDI, and (ii) formation of disulfide bonds in active sites located on the molecular surface causes deformation of the optimum conformation resulting in a decrease in the thermal stability.