Papain, a prototype cysteine protease, was inhibited in a time-dependent manner by azapeptide esters designed to deliver an azaglycine group to the active-site thiol. For example, the rate of inhibition was 18 M-1s-1 for Ac-L-PheAglyOiBu (2) and > 11,000 M-1s-1 for Ac-L-PheAglyOPh (7). The rate of inhibition was slowed in the presence of substrate, and there was no reactivation of the inhibited enzyme after dialysis and incubation in the assay buffer. The inhibited enzyme was completely reactivated after the addition of valine methyl ester. The inhibited form of the enzyme is presumed to be acylated on the active-site thiol. An azaalanine-based peptide inhibited papain much more slowly. Azapeptide alkyl esters are unreactive with serine proteases; therefore, these inhibitors are selective for cysteine proteases.