Further improvements related to the synthesis of peptides containing HmS are presented. Efficient synthetic protocols have been developed to synthesize “difficult” sequences containing a C‐terminal HmS residue, MeA–HmS or consecutive HmS. Preparative methods for orthogonal N‐ and/or C‐protected HmS(Ipr) derivatives are described. Their compatibility with standard solution or solid‐phase peptide chemistry protocols allows synthetic flexibility toward HmS‐containing peptides. In the synthesis of the sterically hindered dipeptides with the C‐terminal HmS(Ipr) residue, HATU proves the highest efficiency, as compared with the fluoride and PyBroP/DMAP coupling methods. The HATU method also outperforms the fluoride activation in the solid‐phase assembly of HmS homosequence. Specific protocols are described to overcome an undesired cyclization to diketopiperazines that occurs during the removal of Fmoc from dipeptides with the C‐terminal HmS(Ipr) or HmS residues, thus precluding their C → N elongation. The successful protocols involve: (i) the 2 + 1 condensation using mixed anhydride activation yielding the desired product with the highest optical integrity or (ii) use of the 2‐chlorotrityl resin as a solid support sterically suppressing the undesired cleavage due to diketopiperazine formation. The latter approach allows the mild conditions of peptide cleavage from solid support, preserving the isopropylidene protection and minimizing the undesired N → O‐acyl migration that was observed under prolonged acid treatment used for cleaving the HmS peptide from the Wang resin. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.