Caspases are a family of cysteine proteases which play a crucial role in apoptosis and inflammation. The involvement of caspases in these processes can be demonstrated by their irreversible inhibition with fluoromethyl ketone and chloromethyl ketone derivatives of peptides resembling the cleavage site of known caspase substrates. These inhibitors irreversibly alkylate the cysteine residue in the active site of caspases. In this study we show that a biotinylated fluoromethyl ketone peptide inhibitor of caspases (z-VAD.fmk) also efficiently affinity-labeled cathepsin B and cathepsin H. In addition, the caspase inhibitors z-VAD.fmk, z-DEVD.fmk and Ac-YVAD.cmk also efficiently inhibited cathepsin B activity in vitro and in tissue culture cells at concentrations that are generally used to demonstrate the involvement of caspases.