Drosophila heat shock factor (HSF) exists as a multimer in solution and when bound to its regulatory element (HSE). We have previously reported evidence that subunits of HSF associate to form homotrimers and that each subunit contacts a conserved 5 bp DNA sequence repeated within an HSE. Here we show that HSF binding is highly cooperative at two distinct levels: between subunits of the HSF multimer, and between multimers. The binding of HSF to one of a pair of adjacent trimeric binding sites facilitates HSF binding to the second by over 2000-fold. This cooperativity is particularly important in binding HSF at 37 degrees C, and could account for the requirement for multiple binding sites in vivo and, in part, for the differential expression of heat shock genes.