We study the effect of microwaves at 2,450 MHz on protein unfolding using surface plasmon resonance sensing. Our experimental method makes use of the fact that unfolding proteins tend to bind to chaperones on their unfolding pathway and this attachment is readily monitored by surface plasmon resonance. We use the protein citrate synthase (CS) for this study as it shows strong binding to the chaperone alpha crystallin when stressed by exposure to excess temperature. The results of microwave heating are compared with the effect of ambient heating and a combination of ambient and microwave heating to the same final temperature. We study the temperature distributions during the heating process. We show that microwaves cause a significantly higher degree of unfolding than conventional thermal stress for protein solutions heated to the same maximum temperature. Bioelectromagnetics 29:324–330, 2008. © 2008 Wiley-Liss, Inc.