The precise pairing of cysteine residues in proteins is routinely achieved in Nature. However, rationally pairing cysteine residues within shorter polypeptides is a long-standing challenge for the preparation of multi-cyclic peptides containing several disulfide bridges. Methods for precisely pairing cysteine residues without extensive manipulation of primary sequence, post-translational modification, or protecting groups would greatly benefit the development of high-quality multi-cyclic peptide therapeutics and targeting ligands. In the first part of this contribution, an efficient and straightforward approach for directing the intermolecular and intramolecular pairing of cysteine residues within peptides using a minimal CXC motif will be presented.[1] Orthogonal disulfide pairing can be exploited in complex redox media to rationally produce dimeric peptides and bi/tricyclic peptides from fully reduced peptides containing 1–6 cysteine residues. In the second part of this contribution, strategies that exploit intermolecular twin-disulfide pairing between two peptides and that between peptides and small dithiol molecules for the development of α-helical peptides with ultrahigh structural and proteolytic stability will be presented.[2-4] We will show how the interplay of disulfide bonds, α-helicity, and noncovalent interactions regulates the structural and proteolytic stability of peptides. Finally, our efforts to exploit the orthogonal disulfide pairing between cysteine and penicillamine (or other unnatural thiol-containing amino acids, UTAA) for regulating the folding and cyclization of peptides will be discussed.[5] We will introduce how the geometric strain of disulfides and steric hindrance during thiol-disulfide exchanges can be rationally manipulated to achieve precise disulfide pairing. Our results demonstrated that rational replacement of cysteine residues within peptides by UTAAs can leads to formation of multi-cyclic peptides with unique disulfide pairing patterns without the problem of isomerization in complex redox buffers or in biological fluids.