Quantum dots (QDs) CdS and CdSe were synthesized in three different media including reverse micelles, aqueous solution, and trioctylphosphine oxide/trioctylphosphine (TOPO/TOP). Transmission electron microscope (TEM), X-ray diffraction (XRD), UV-VIS, fluorescence spectroscopy and microscopy were used to characterize the QDs and their nanoassemblies. CdS QDs synthesized in reverse micelles showed broad emission spectra. CdSe-CdS QDs with core shell structure synthesized in aqueous solution showed more than 30% emission quantum yield. CdSe-CdS QDs of different emission colors were prepared. CdSe and CdSe-ZnS QDs were also synthesized in TOPO/TOP media. This synthesis route produced highly luminescent CdSe QDs with over 50% emission quantum yield. The application of QDs as ions probes and methods to encapsulate QDs in nanospheres including micelles, glyconanospheres and silica nanospheres and the use of these nanospheres in bioassays are described. CdS QDs capped with different ligands such as thioglycerol, cysteine and polyphosphate showed different responses to biological relevant ions. The emission intensity of polyphosphate capped CdS QDs was affected by all the tested ions and did not show a selective response. On the other hand, the emission of thioglycerol capped CdS QDs was selectively quenched by copper ions while the emission of cysteine capped CdS QDs was selectively enhanced by zinc ions. Stern-Volmer equation was applied to correlate the emission intensity of the CdS QDs and the copper ion concentration. A Lagmuir isotherm binding equation was used to describe the relation between the emission intensity of cysteine capped CdS QDs and zinc ion concentration. The possible mechanism to explain the effects of capping ligands on CdS QDs responses to ions is also discussed. CdSe QDs synthesized in TOPO/TOP media were encapsulated in nanospheres for bioassay applications. The glyconanospheres contained a large number of glucose residues on their surface and showed high binding activity towards the lectinic protein Concanavalin A (Con A). Silica nanospheres containing hundreds of CdSe QDs were functionalized with thiol groups to enable the conjugation of streptavidin to the nanospheres. The streptavidin modified silica nanospheres were used as luminescent indicators in a sandwich immunoassay for the detection of antiprotein A antibody. The advantages and disadvantages of the nanospheres based bioassay are discussed.