The spectroscopic properties of CdSe/ZnS quantum dots (QDs) were observed to change as a function of thioalkyl acid ligand. Experiments were performed using 2, 3, 6, and 11-carbon linear thioalkyl acids, as well as mercaptosuccinic acid (MSA) and dihydrolipoic acid (DHLA). Bathochromic shifts of up to 14 nm in the emission spectra of QDs capped with these ligands were observed. Similarly, hypsochromic or bathochromic shifts up to 7 nm were observed for a specific ligand in acidic or basic solution, respectively. These shifts could be correlated to the number of ionized ligands and the ability of the ligands to act as hole acceptors. It was also found that differences in quantum yield between the ligands were primarily due to variations in radiative decay rate and not nonradiative decay rate. This indicated that different degrees of QD surface passivation were not responsible for the differences, and that the radiative system must be considered as the sum of the ligands and the QD nanocrystal. The stability of QDs capped with mercaptoacetic acid, MSA, and DHLA towards aggregation at low pH was found to correlate with the pK(a) of the ligands. Spectral shifts were also observed during aggregation. Overall, the luminescence of thioalkyl acid capped QDs appears to be a complex function of dielectric constant, electrostatic or hole-acceptor interactions with ionized ligands, and, to a lesser extent, passivation.