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Abstract: Molecularly imprinted polymers (MIPs) are highly crosslinked polymers that can be readily tailored with recognition properties and have been used in separation, sensing and catalytic applications. Unfortunately, molecular imprinting is commonly a low fidelity process, yielding only small increase in the number of the desired high affinity binding sites. We have measured this binding site heterogeneity in MIPs and the effects of changing different variables in the imprinting process. Quantitative analysis of the distribution of sites has allowed us to more accurately predict and compare the binding properties of MIPs. It has also lead to some surprising conclusions about the nature of the imprinting process. The increase in high affinity sites in MIPs actually appears to arise from an increase in heterogeneity. This observation suggests that MIPs are poor materials for chromatography and catalysis and maybe better suited to applications such as sensing and scavenging that are not as sensitive to heterogeneity.