In this thesis, luminescent lanthanide-doped nanocrystals, and lead-based quantum dots nanocrystals are explored as alternative bioimaging agents to fluorescent proteins and organic fluorophores for deep-tissue imaging. The first chapter gives a brief introduction on the aforementioned nanocrystals and their special optical properties. In chapter 2 the simple changes in the drying and baking temperature of the Yb3+ and Ho3+ doped LaF3 nanocrystals-silica sol-gel mixture aid in the explanation of the formation of two types of silica. The difference in the phonon energies of the two types of silica is found to control effectively the ratio of red to green emissions obtained from the upconversion process. However, the nanocrystals do not disperse in water making them unsuitable for bioimaging. Chapter 3 describe the synthesis of NaYF4 nanocrystals doped with Yb3+/Er3+ or Yb3+/Tm3+ ions followed by two surface modification strategies (intercalation and crosslinking) to disperse them in physiological buffers and biological growth media. Of the two methods, the crosslinked polymer coating of the nanocrystals alone exhibits stability in aforementioned media. In chapter 4 the applicability of lanthanide-doped NaYF4 nanocrystals are studied as bioimaging agents in two-photon upconversion laser scanning microscopy for deep-tissue imaging. Their performance as bioimaging agents was not better than fluorescent proteins and organic molecules. On the other hand with two-photon upconversion wide field microscopy (TPUWFM), brain blood vessels over a depth of 100 µm could well be separated. Furthermore, with the 800 nm emission from Tm3+ ions one can image twice as deep as the green emission with TPUWFM. In chapter 5, probing the NaYF4 nanocrystals with energy-dependent XPS shows that, the Y3+ ions on the surface of the nanocrystals are different from the ones present inside the nanocrystals. This chapter is concluded with a preliminary investigation of Yb3+ and Tm3+ doped NaYF4 with resonant XPS. Chapter 6 examines four different types of surface modification strategies to transfer hydrophobic lead-based quantum dots to physiological buffers and biological growth media. Of the four methods, the crosslinked polymer coating of quantum dots alone exhibits colloidal stability and the QDs retain their luminescence in aforementioned media over several months. The conclusions and future outlook for the work are elucidated in chapter 7. / Graduate