Semiconductor inorganic nanocrystals or quantum dots (QDs) are nowadays extensively used for imaging and analysis of bio-molecules owing to their superior optical properties over conventional organic fluorophores. They have excellent potential for synthesizing molecular probes against various biological markers such as free antigens, cell surface markers/antigens, bacteria, viruses and tissues. Traditional synthesis protocols of the QDs generally lead to the formation of hydrophobic nanocrystals. For biological applications, post-synthesis modifications need to be introduced to render required hydrophilicity. However, such additional steps make the tiny QDs structures bulky, which is unwanted in subsequent in-vivo executions. The present work reports a simple method for the direct synthesis of hydrophilic carboxyl (–COOH) functionalized CdS QDs using mercaptopropionic acid as a sulfur source and stabilizer. This aqueous synthesis route avoids the requirement of extra surface modification steps. The size and surface morphology of the synthesized CdS QDs were studied by electron microscopy. The average diameter of the QDs has been found to be in the range of 2-3.5nm. Spectral studies confirmed the grafting of –COOH terminal on the synthesized nanocrystals. Band gap energy and the theoretical size of the particles were calculated and found in good agreement with the experimental analysis. Due to the size quantization effect, the estimated band gap energy (2.6eV) of the QDs was on a higher side than that reported (2.4eV) for the bulk material. The synthesized nanocrystals can be further conjugated with bio-molecules for high-throughput drug screening, clinical immunological assays and protein-protein interaction studies.