Molecularly imprinted polymers hold great promise for the separation of chiral compounds. A non-covalent approach to the synthesis of MIPs relies on the presence of specific and non-specific interactions, which lead to the formation of a molecular imprint. The structural differences between 17-alpha-estradiol and 17-beta-estradiol are too small to permit their efficient separation on a MIP prepared with beta-estradiol as a template. Molecular modeling revealed the presence of only one hydrogen bond that differentiates the two isomers.