Bovine alpha(1)-acid glycoprotein (bAAG) and bovine serum albumin (BSA) are plasmatic acceptors working as carriers by the specific and reversible binding of several drugs in vivo. We synthesized affinity columns by coupling bAAG and BSA to an activated chromatographic support through their carbohydrate moieties, to preserve protein tertiary structure and, consequently, to improve the biological activity in vitro. The bAAG and BSA affinity columns were used to study the binding of acidic and basic drugs. Moreover, a purification strategy was developed for the cleanup of drug residues from biological matrices and foods, prior to screening and/or confirmatory analysis, on the basis of the specific molecular recognition between the protein and the drug. The aim of this work was to test the potency of bAAG- and BSA-based affinity chromatography to bind some veterinary drugs and purify them in the context of the official control of animal products. The efficiency of these homemade affinity columns in minimising matrix interference and in selective cleanup of different classes of substances was reported and discussed.