The influence of thioalkyl acid ligand was evaluated during aqueous synthesis at 100 °C and under hydrothermal conditions (150 °C) of CdTe and CdSe quantum dots (QDs). Experiments performed with 3-mercaptopropionic acid (MPA), 6-mercaptohexanoic acid (MHA) and 11-mercaptoundecanoic acid (MUA) demonstrated that the use of MHA and MUA allowed for the preparation of very small nanoparticles (0.6-2.5 nm) in carrying out the reaction under atmospheric pressure or in an autoclave and that the photophysical properties of QDs were dependent on the ligand and on the synthesis conditions. The influence of various experimental conditions, including the Te-to-Cd ratio, temperature, and precursor concentration, on the growth rate of CdTe or CdSe QDs has been systematically investigated. The fluorescence intensities of CdTe QDs capped with MPA, MHA, or MUA versus pH were also found to be related to the surface coverage of the nanoparticles.