Here we demonstrate a simple, template-free approach to the formation of spherical gold aggregates through the reduction of HAuCl4 by NaBH4, in the presence of cysteine (Cys) as a capping agent. The resulting aggregates are quite stable in solution. The pH of the solution and the molar ratio of Au:Cys are two key empirical factors in the formation of such highly ordered aggregates. At slightly alkaline pH (7–10) and with Au:Cys ratios ranging from 1:0.5 to 1:2, spherical Au aggregates of 30–80 nm are formed. At lower Cys ratios (Au:Cys≥1:0.5) very loosely linked aggregates are formed; however, at very high Cys ratios (Au:Cys≤1:3), highly dispersed Au particles of 2–4 nm are obtained, which are virtually indistinguishable from the original colloidal form. Aggregate size is influenced markedly by component concentration; a 3-fold increase in standard levels resulted in Au spherical aggregates of a larger size, 200–500 nm. In addition, we used a combination of Cys and lysine (Lys) as a capping agent/cross-linker and found that the morphology of the Au colloid aggregates can be easily manipulated from a linear to a spherical form by adjusting the proportions of Cys and Lys in the capping agent/cross-linker mixture. The introduction of mercapto (SH)-containing organic acids reduced the cross-linking ability of Cys, especially in the case of long-chain acids. Complete disruption of the spherical aggregates highlights the importance of Cys per se. An explanation of this ordered self-assembly process is proposed, in the context of the known surface chemistry of Au colloids.