Activation of the caspase family of cysteine proteases results in the deregulation of cellular homeostasis and apoptosis. This deregulation is a key factor in the development of Alzheimer's disease, Parkinson's disease, and cancer. Thus, the caspases are important drug targets for the therapeutic intervention of a number of pathological states involving inflammation and apoptosis. In this article, we report the results of inhibition kinetics and binding studies utilizing fluorescence spectroscopy and isothermal titration calorimetry to characterize the mechanism of interaction of caspase-3 with three different classes of inhibitors: peptidomimetics, isatins, and pyrimidoindolones. The peptidomimetics and pyrimidoindolones bind to both active sites of the caspase-3 homodimer with equal affinity and favorable enthalpic and entropic binding contributions. Enzyme activity is abolished when both active sites are occupied with the above inhibitors. In contrast, the isatins bind to caspase-3 with significant heat release (-12 kcal/mol) and negative entropy. In addition, enzyme activity is abolished upon isatin binding to one active site of the homodimer resulting in half-site reactivity. Our studies provide important mechanistic insight into inhibitor interactions with caspase-3 and a way to characterize inhibitor interactions that may not be readily apparent from the crystal structure.