Nanoparticles have attracted attention as a scaffold to obtain smart biomaterials because of several advantages: Firstly, the biodistribution of the nanoparticles can be modulated by changing the size of the particles. For example, as we presented in this paper, silica-based nanoparticles are versatile materials for designing functional bioprobes and the vesicles for drug delivery because of their high stability and the flexibility in the modification. Because various size and surface-modified silica nanoparticles can be readily prepared, we can deliver drugs or other bioactive materials to the target sites by loading onto the nanoparticles with the size effects on the distribution. In particular, nanoparticles in the range of 20 nm to 400 nm in diameter show tumor-selective integration known as the enhanced permeability and retention (EPR) effect. 1-7 Therefore, the site-specific delivery can be realized based on the preprogrammed designs. Secondly, the local concentrations of the loaded drugs can be readily enhanced. In the case of the drugs with small molecular weights, the drug concentrations could be lowered by the diffusion. On the other hand, since the nanoparticles have better retention ability than those of small molecules, it is relatively easy to keep the local concentration to receive enough drug efficiency. In addition, if the nanoparticle can slowly release the loaded drugs, the sustained release system can be readily realized. Thirdly, the diverse properties can be obtained not only originated from the intrinsic properties of the component elements or the surface modification but also from the nano-sized effects of the particles. For example, the nanoparticles composed of ferromagnetic iron oxide show similar behaviors, called superparamagnetism, to the paramagnetic materials such as no hysteresis and no residual magnetization. 8,9 These materials are used as a conventional contrast agent in magnetic resonance imaging (MRI). In the case of gold nanoparticles, the absorption bands in the visible region can be observed. Various kinds of biosensors have been invented based on the gold nanoparticles. The nanoparticles composed of semiconductor materials called as quantum dots show various emission colors depended on their diameters. 10-13 Based on these characteristics derived from the size effects, unique optical bioprobes have been developed. In this review, we survey the functionalized nanoparticles for the application in nanobiotechnology. Our recent studies on the development of bioprobes or bio-related materials with the series of nanoparticles composed of iron oxide, silica and gold are mainly introduced. The typical synthetic procedures are also described in the latter part. Superparamagnetic iron oxide MR sensors for biomolecules Initially, we present the superparamagnetic iron oxide (SPIO)-based contrast agents in magnetic resonance imaging (MRI). MRI is one of the powerful and conventional diagnostic tools in modern clinical medicine for the 3D visualization inside vital bodies with high res...