A protocol is reported for the preparation of water-soluble, thiol-protected Au nanoparticles (Au-MPC) where dioctylamine is used as a stabilizing agent when the gold cluster is formed using the two-phase Brust and Schiffrin procedure. The amount of amine controls the size of the nanoparticles in the 1.9-8.9 nm diameter range. The final stabilization of the gold clusters by addition of functionalized thiols is performed under very mild conditions compatible with most biomolecules. The procedure is suitable for a wide variety of functional groups present in the thiol and allows one to use thiol mixtures with a precise control of their composition in the monolayer. As a proof of principle, examples of nanoparticles protected with thiols comprising functional groups ranging from polyethers, saccharides, polyamines and ammonium ions are reported.