A new surface chemistry has been developed for the solubilization and biofunctionalization of inorganic semiconductor nanocrystals fluorescent probes, also known as quantum dots. This chemistry is based on the surface coating of quantum dots with custom-designed polycysteine peptides and yields water-soluble, small, monodispersed and colloidally stable probes that remain bright and photostable in complex biological milieus. This peptide coating strategy was successfully tested on several types of core and core-shell quantum dots emitting from the visible (e.g. CdSe/ZnS) to the NIR spectrum range (e.g. CdTe/CdSe/ZnS). By taking advantage of the versatile physico-chemical properties of peptides, a peptide "toolkit" was designed and employed to impart several biological functions to individual quantum dots and control their biochemical activity at the nanometer scale. These biofunctionalized peptide-coated quantum dots were exploited in very diverse biological applications. Near-infrared emitting quantum dot probes were engineered with optimized blood circulation and biodistribution properties for in vivo animal imaging. Visible emitting quantum dots were used for single molecule tracking of raft-associated GPI-anchored proteins in live cells. This last application revealed the presence of discrete and non-caveolar lipid microdomains capable of impeding free lateral diffusions in the plasma membrane of Hela cells. Imaging and tracking of peptide-coated quantum dots provided the first direct evidence that microdomains having the composition and behavior expected for lipid rafts can induce molecular compartmentalization in the membrane of living cells.