Core shell molecularly imprinted polymers (CS-MIPs) have been prepared by aqueous emulsion polymerization using water soluble template molecules. An amphiphilic binding monomer, oleyl phenyl hydrogen phosphate and ethylene glycol dimethyl acrylate were used in the formation of highly crosslinked surfaces around divinyl benzene crosslinked polystyrene core colloids. Evidence was obtained by transmission electron microscopy (TEM) for a change in surface morphology when the polymer shell was formed in the presence of a template. The caffeine imprinted polymers were shown to bind caffeine in preference to theophylline from an equimolar mixture of the compounds in aqueous solution at pH 7.0, whilst concentration-binding (Scatchard) curves revealed the presence of two populations of binding sites in aqueous phosphate buffer at pH 8.0 for caffeine and theophylline. Similar studies were also carried out for (S)-propranolol and (S)-atenolol at pH 5.5, which also revealed the presence of two populations of binding sited for core-shell particles imprinted with these compounds (S)-Propranolol was selectively removed from a solution of (S)-propranolol and (S)-atenolol by both of the CS-MIPs, whereas the non-imprinted particle showed no selectivity for either component.