Binding affinities are useful measures of target interaction and have an important role in understanding biochemical reactions that involve binding mechanisms. Surface plasmon resonance (SPR) provides convenient real-time measurement of the reaction that enables subsequent estimation of the reaction constants necessary to determine binding affinity. Three models are considered for application to SPR experiments the well-mixed Langmuir model and two models that represent the binding reaction in the presence of transport effects. One of these models, the effective rate constant approximation, can be derived from the other by applying a quasi-steady state assumption. Uniqueness of the reaction constants with respect to SPR measurements is considered via a structural identifiability analysis. It is shown that the models are structurally unidentifiable unless the sample concentration is known. The models are also considered for analytes with heterogeneity in the binding kinetics. This heterogeneity further confounds the identifiability of key parameters necessary for reliable estimation of the binding affinity. (C) 2012 Elsevier Ltd. All rights reserved.