It is well known that selectivity of molecularly imprinted polymers (MIPs) depends on adequate choice of functional monomer before the experimental synthesis. Computational simulation seems to be an ideal way to produce selective MIPs. In this work, we have proposed the use of semi-empirical simulation to obtain the best monomer able to strongly interact with ciprofloxacin. Twenty functional monomers were evaluated through semi-empirical quantum chemistry method and three MIPs were synthesized using the monomers acrylamide (M5), acrylic acid (M4) and 1-vinylimidazole (M16), yielding the maximum adsorption capacities of 282.0, 223.8 and 202.5 μmol g-1, respectively, as predicted by the computational simulation. From competitive adsorption studies in the presence of structurally similar compounds, the MIP synthesized with acrylamide was found to possess higher specific selectivity factors (S) if compared to non-imprinted polymer (NIP), thus indicating good recognition selectivity for the ciprofloxacin.