The nature of molecular recognition in an imprinted polymer that is formed by the self-assembly of binding monomer and imprint through noncovalent interactions is investigated. The system studied uses ethylene glycol dimethacrylate, methacrylic acid, and L-phenylalanine anilide as the crosslinking monomer, binding monomer, and imprint, respectively, to assemble the imprinted polymer. A proposal for the self-assembly mechanism between the binding monomer and imprint that occurs during polymer synthesis is derived from a single-crystal X-ray structure of a crystal containing binding monomer and imprint and from H-1 NMR and FTIR spectroscopy of solutions of these components. These studies show the presence of a salt-bridge interaction that leads to a 1:1 molecular complex between methacrylic acid and L-phenylalanine anilide and provide no evidence for the formation of higher-order molecular complexes of these species. Furthermore, macroscopic phase separation is observed between the imprint and binding monomer and the cross-linking monomer in this system prior to and after polymerization. These findings suggest a mechanism for enantioselective molecular recognition in the imprinted polymer involving remaining, occluded imprint molecules, which can provide for binding via imprint-imprint intermolecular interactions. Support for this mechanism is provided from polymers prepared using a combination of imprint and mimic, L-phenylalanine 4-vinylanilide; the latter remains covalently bound in the polymer and is shown to increase the rebinding of imprint while not significantly affecting the binding of the opposite enantiomer. The proposed mechanism provides insight into the nature of binding site heterogeneity in imprinted polymer systems.