Endotoxin or lipopolysaccharide (LPS) contamination in proteins expressed by Gram-negative bacteria is a major drawback associated with protein expression. Endotoxin intoxication in humans and animals above a certain threshold level can result in a fatal immune response. Reduction in endotoxin levels is therefore essential before proteins can be used in in vivo studies or sold as pharmaceutical products. Affinity chromatography employing the peptide Polymyxin B (PMB) as an affinity ligand is one way in which endotoxin contamination has been addressed; this is, however, a costly process. We describe the synthesis of a novel affinity ligand based on the structure of the drug pentamidine, which can be applied effectively in endotoxin removal. The synthetic route to this ligand is straightforward and inexpensive, while the ligand can be readily immobilized onto activated sepharose beads. Thus, we demonstrate that these pentamidine affinity beads bind endotoxin/LPS with comparable capacity to PMB affinity systems, that the beads can be recycled efficiently and economically without loss of binding capacity, and application of the functionalized beads for endotoxin removal in an authentic contaminated antibody sample.