Recently, different types of nano-scaled particles designed to carry diagnostic and therapeutic functions have been synthesized and characterized for their possible biomedical applications in the body. These nanoparticles could be organic, inorganic, biological or composite. Despite the exciting progress from the multidisciplinary efforts including the disciplines of chemistry, physics and material science, a major factor has been easily overlooked along the path for successful translation of these excitements to the real applications of practical clinical value; the factor is the physiological whereabouts and fates of these nanoparticles in the body. What is the immediate and prolonged body distribution of these nanoparticle ? Will these nanoparticles be cleared from the body and via what mechanisms or they will tend to stay in for a long time (particularly those inorganic-based nanoparticles)? Will these nanoparticles metablizable, if yes, will the following metabolized products safe and how would they be finally taken care of in the body? What are the acute and chronic biological effects will these nanopartiles have on the body ? How will the size and surface chemistry of the nanoparticles be correlated with the physiological fate of the nanoparticles in the body ?? The author would like to present the results from the interdisciplinary teamwork on in vivo investigations on the physiological whereabouts and fates of the nanoparticles; using quantum dots and mesoporous nanosilicates as the model compounds.