Colloidally prepared semiconductor nanocrystal quantum dots (QDs) are inherently incompatible with biological systems because of the native hydrophobic molecules that coat their surfaces. Post-synthetic techniques such as ligand exchange and encapsulation are therefore employed to make them soluble in aqueous media while preserving their valuable properties such as bright photoluminescence and stability. Small hydrophilic organic molecules like dihydrolipoic acid and tris(hydroxypropyl)phosphine are used to displace the hydrophobic surface ligands, and derivatization by carbodiimide bioconjugation can enhance pH stability. Several QD encapsulation methods in polymer shells are covered, with the most promising one involving the use of a four-stream vortex mixer to create QD-embedded polymer microspheres with a small size distribution and high fluorescence intensity. The ability of polyhistidine tags to self assemble onto QDs via metal coordination interactions is also exploited to attach dye-labeled protein molecules onto QD surfaces so as to perform fluorescence resonance energy transfer investigations.