Biomodified CdS nanoparticles were synthesized using L-cysteine as a capping agent in the colloidal state as a function of pH. The role of pH on the size and structure of CdS nanoparticles was investigated in detail. At pH 7.4 and 9.1, X-ray diffraction spectra of as prepared samples showed the presence of a mixture of cubic and hexagonal phases while cubic phase was formed at pH 11.2. A gradual transition to the hexagonal phase was observed for refluxed samples at pH 9.1 and 11.2. Whereas, at pH 7.4, the sample remains in a mixture of cubic and hexagonal phase even after refluxing. The particle size of as prepared samples was about 2 nm, and for refluxed samples the size increased up to 10 nm. The binding of cadmium through thiol group is evidenced by infrared spectra. An intense band due to C-C-N vibration was observed after 24 h of reflux. The formation of a specific molecular cluster determines the growth of a particular phase. Transmission electron microscopy (TEM) studies support the X-ray diffraction (XRD) studies and exhibit well separated spherical particles while refluxed samples show clustering.