Macrocycles provide an attractive modality for drug development but the identification of ligands to targets of interest is hindered by the lack of large macrocyclic compound libraries for high-throughput screening. A strategy to efficiently synthesize large numbers of macrocyclic compounds is based on the cyclization of peptides having thiol groups at both ends (dithiol peptides) by bis-electrophile reagents. Herein, I have established a strategy to produce macrocyclic compounds at high-throughput in a 96-well format, comprising the steps of i) peptide synthesis on solid phase immobilized via a disulfide bridge, ii) side-chain deprotection on solid phase, iii) reductive peptide release from solid phase, iv) removal of reducing agent by evaporation, and v) cyclization of the peptides by addition of bis-electrophiles. In contrast to a related strategy for dithiol peptide synthesis based on cyclative release, the new strategy allows for the synthesis of particularly short dithiol peptides and thus accessing macrocycles smaller than 600 Da that are attractive for the development of orally available and/or cell permeable drugs.