Because Congo red (CR) can bind to critical intermediate structural forms of amyloid beta (Aβ), it has been suggested as a potential therapeutic agent against neurodegenerative disorders such as Alzheimer's disease. In this study, the interaction of CR with Aβ(12-28) was investigated by use of isothermal titration calorimetry (ITC). Studies conducted between 15 and 35 °C show that binding of CR to Aβ(12-28) was strongly dependent on temperature, with a decrease in CR-Aβ(12-28) complexation as temperature increases, presumably because of conformational changes within Aβ(12-28) at the highest temperatures, that conceal the CR binding sites. In fact, no CR binding was observed at 35 °C. The binding of CR to Aβ(12-28) was associated with favorable changes in both enthalpy and entropy that resulted in binding constants (K) of between 10(5) and 10(6) M (-1). An early (and more intense) entropy-driven CR disaggregation phase (K ~10(7)-10(8) M (-1)) was observed before the onset of CR-Aβ(12-28) complexation. Only CR disaggregation was observed at 35 °C. These results may provide further insights into the ability of CR to inhibit Aβ toxicity in neurodegenerative diseases.