A novel experimental system to distinguish between potential thermal and non-thermal effects of electromagnetic fields (EMFs) on the conformational equilibrium and folding kinetics of proteins is presented. The system comprises an exposure chamber installed within the measurement compartment of a spectropolarimeter and allows real-time observation of the circular dichroism (CD) signal of the protein during EMF exposure. An optical temperature probe monitors the temperature of the protein solution at the site of irradiation. The electromagnetic, thermal, and fluid-dynamic behavior of the system is characterized by numerical and experimental means. The number of repeated EMF on/off cycles needed for achieving a certain detection limit is determined on the basis of the experimentally assessed precision of the CD measurements. The isolated thermosensor protein GrpE of the Hsp70 chaperone system of Eschericha coli serves as the test protein. Long-term experiments show high thermal reproducibility as well as thermal stability of the experimental setup. Bioelectromagnetics. 34:419-428. © 2013 Wiley Periodicals, Inc.