AbstractHeat shock transcription factors (HSFs) of higher eukaryotes respond to physical and cellular stress signals by tri‐merizing, binding to a specific site on DNA, and transactivating genes encoding the heat shock proteins. In this work, limited proteolysis was used as a biochemical probe of the domain organization of Drosophila HSF. Both unshocked monomelic and heat‐shocked trimeric HSF possess an internal protease‐sensitive region located between the aminoterminal and carboxyl‐terminal hydrophobic heptad repeats, suggesting that this is a less structured region compared to those defined for DNA‐binding, trimerization, and transactivation. For a few cleavage sites, the heat‐shocked form of HSF is more accessible to proteases than the unshocked form, providing an additional diagnostic marker for inducible changes in conformation or modification between the latent and activated forms of HSF.