The interaction of gold nanoparticles (AuNPs) with cysteine and its derivatives is the basis of a number of bionanotechnologies, and for these, the most important process is aggregation (or antiaggregation), which enables an array of colorimetric detection methods. When AuNPs were functionalized with cysteine, its dimer cystine, or the cysteine-derived tripeptide, glutathione, three different mechanisms of aggregation were observed. Both cysteine and glutathione induced aggregation of AuNPs without further pH modification: the first by interparticle zwitterionic interaction and the second by interparticle hydrogen bonding. Cystine, however, did not induce aggregation, although it dissociated into two cysteinate moieties upon adsorption on the AuNPs, which appear to be chemically identical to cysteinate produced from cysteine adsorption. We show that the difference is due to the lower coverage of cysteinate from cystine and differences in charge states of the adsorbates. On modifying the pH to 1.5, the surface species become cationic (neutral COOH and protonated NH3+), and aggregation of cystine/AuNPs occurs immediately by interparticle hydrogen bonding. Thus, cysteine may induce aggregation by neutral hydrogen bonding or zwitterionic interaction between nanoparticles, but the mechanism depends sensitively on a number of parameters.