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The selective deprotection of Lys(Mtt)‐containing peptidyl resins was successfully monitored by RP‐HPLC using very short linear gradients. RP‐HPLC analyses of the acidic filtrates also revealed the partial cleavage of the Trt groups and of the peptide–resin bond. The absorbance of the Mtt carbocation at 470 nm is only twice that of the Trt cation. Thus, the UV monitoring at 470 nm seems to be inappropriate, especially at the end of the deprotection, when the Mtt and the Trt levels are comparable. Copyright © 2000 European Peptide Society and John Wiley & Sons, Ltd.