A high-throughput method has been developed for the synthesis of a series of highly cross-linked cyclodextrin-based photo-polymers (CDPs). The synthesis is carried out in a multiwell format using an acryloyl beta-cyclodextrin (average 3.4 acryloyl functions per macrocycle) and 1-hydroxycyclohexyl phenyl ketone as a photoinitiator. A number of additional monomers (acrylamide, N-isopropylacrylamide, 2-hydroxyethyl methacrylate, 2-vinylpyridine, acrylic acid, itaconic acid, and 2-acrylarnido-2-methyl-1-propanesulfonic acid) and cross-linkers (divinylbenzene, ethylene glycol dimethacrylate, and trimethylolpropane trimethacrylate) have been added to the formulation at different molar ratios. The binding properties of the produced polymers of a mixture of molecules of interest (acetaminophenol, atenolol, caffeine, ofloxacin, ciprofloxacin, tetracycline, sulfamethoxazole, chloramphenicol, (+/-)-propranolol, and diclofenac) have been assayed in water using an HPLC-based high-throughput method. It is demonstrated that the binding properties of the produced polymers can be tuned by the monomers used for the synthesis. They arise not only from the ability of the cyclodextrin macrocycle to include the target compounds in its cavity but also from a set of additional synergistic interactions between the polymer and the targets. Two selected formulations have been up scaled at the grain quantity; the binding results show a similar behavior than the CDPs produced using the high-throughput method.