Three novel affinity columns were evaluated for purification of rat and pig squalene epoxidase (SE). Pig SE was adsorbed to a resin hearing an N-cyclopropyl-N-trisnorsqualenamine (TNS-CPA) type functionality, and eluted with 25 mM KCl to give a 55-56 kDa doubler, whereas rat SE required the use of N-methyl-N-trisnorsqualeneamine (TNS-MA) affinity resin. Rat SE could be eluted with 0.5M KCl, to give a single band at 52 kDa. Squalene epoxidase (SE) (EC 1.14.99.7) catalyzes the conversion of squalene to (3S)-2,3-oxidosqualene. This reaction and the subsequent cyclization of (3S)-2,3-oxidosqualene by oxidosqualene cyclase (OSC) to lanosterol are the key steps in cholesterol biosynthesis in vertebrates. SE has been the focus of efforts to develop hypocholesterolemic, herbicidal and antifungal agents. To this end, we have developed a method of purifying vertebrate SE by affinity chromatography, which makes use of the very strict substrate requirements for SE to achieve bioselective adsorption. Potent slow, tight-binding inhibitors are used to achieve bioselective elution.