Enantiomeric 1-acetamido boronic acids, which are N-acetyl transition state analog inhibitor analogs of L- and D-forms of the amino acids alanine, phenylalanine, p-fluorophenylalanine, p-chlorophenylalanine, and 1-naphthylalanine, have been evaluated as inhibitors of the serine proteases subtilisin Carlsberg (SC) and alpha-chymotrypsin (CT). All of the boronic acids are powerful competitive inhibitors of both enzymes, with, as expected, the L-enantiomers being generally more potent than the D-enantiomers. However, a dramatic reversal of the normal stereoselectivity preference was observed in the inhibition of CT by [1-acetamido-2-(1-naphthyl)ethyl]boronic acid, with the D-enantiomer becoming a 25-fold more potent inhibitor than the L-enantiomer. Furthermore, the K-I of 127 nM for CT inhibition by this D-enantiomer is the lowest of any of the boronic acids evaluated. Molecular modeling analyses of the possible binding modes of the inhibitors suggest that the stereoselectivity reversal is due to S-1-pocket orientations of naphthyl groups that are different from those of the aromatic side chains of the phenylalanine analogs.