Ultrasensitive, isothermal titration calorimetry was used to generate thermodynamic data to assess the binding properties of molecularly imprinted polymer microgels. Microgels were imprinted using L-boc-phenylalanine anilide (L-BFA) and then utilized in binding experiments with a variety of probe molecules, structurally closely related to the template molecule. Significant differences were observed between the binding enthalpy of the original template L-BFA and those of D-BFA, L-boc-phenylalanine, L-boc-tryptophane, and L-boc-tyrosine.