Clenbuterol molecularly imprinted polymer microbeads were prepared with a two-step swelling and thermal polymerization technique with either methacrylic acid or acrylamide (AAm) as the monomer and ethylene glycol dimethacrylate as the crosslinker at different monomer/crosslinker ratios. The quality of the microbeads, in terms of shape, size distribution, rigidity, and monomer incorporation, was evaluated as a function of the reaction parameters. A good imprinting effect was obtained with both systems, as assessed by high-performance liquid chromatography (HPLC) experiments with phosphate-buffered saline/acetonitrile eluents, with a complete baseline separation of clenbuterol with respect to other beta-adrenergic agents obtained. When AAm was used as the monomer, improved control of the polymerization process was achieved, producing microbeads with lower polydispersity and no lack of separation capacity.