Peptidyl chloromethyl ketones, largely derived from arginine, inactivate cathepsin B (beef spleen) at rates that vary 300 fold according to sequence, but the residue in the P1 position is not responsible for this variation since homoarginine or nitroarginine in this position provide inhibitors as good or better than those containing arginine. Peptidyl chloromethyl ketones containing hydrophobic residues such as phenylalanine or valine in the P2 and P3 position are the most effective inhibitors of the group. Cystamine (bis-aminoethyl disulfide) inactivates cathepsin B by formation of a mixed disulfide. Derivatives of cystamine containing phenylalanine, such as bis-N,N'-Phe-cystamine and bis-N,N'-Ala-Ala-Phe-cystamine are more effective and represent a new class of affinity labels for cathepsin B. Immobilized peptidyl cystamine derivatives can be used for the purification of cathepsin B by covalent affinity chromatography. Cathepsin B from beef spleen has a pronounced carboxydipeptidase action on glucagon as described for the human liver enzyme. This action can be conveniently followed by high pressure liquid chromatography.