We report on the synthesis and microstructural and microanalytical analysis of dodecanethiol and benzylthiol-stabilized Au nanoparticles (diameter range between 2 nm and 10 nm). Stable functionalized gold nanoparticles were synthesized by using two different routes: a two-phase liquid-liquid method and a one-phase method. The size, strain, shape and crystalline structure of the nanocrystals were determined by a full-pattern X-ray powder diffraction analysis and high-resolution electron microscopy. The chemical environment of the Au nanocrystals and their interaction with the thiols was investigated by X-ray photoelectron spectroscopy. Photoluminescence spectroscopy measurements show a characteristic IR emission at λ=960 nm of small sized Au nanocrystals (∼3 nm). The origin of this IR emission line seems to be correlated to the Au-S bonding and the size of the nanoparticles.