The use of nanoparticles for the early detection, cure, and imaging of diseases has been proved already to have a colossal potential in different biomedical fields, such as oncology and cardiology. A broad spectrum of nanoparticles are currently under development, exhibiting differences in (i) size, ranging from few tens of nanometers to few microns; (ii) shape, from the classical spherical beads to discoidal, hemispherical, cylindrical, and conical; (iii) surface functionalization, with a wide range of electrostatic charges and biomolecule conjugations. Clearly, the library of nanoparticles generated by combining all possible sizes, shapes, and surface physicochemical properties is enormous. With such a complex scenario, an integrated approach is here proposed and described for the rational design of nanoparticle systems (nanovectors) for the intravascular delivery of therapeutic and imaging contrast agents. The proposed integrated approach combines multiscale/multiphysics mathematical models with in vitro assays and in vivo intravital microscopy (IVM) experiments and aims at identifying the optimal combination of size, shape, and surface properties that maximize the nanovectors localization within the diseased microvasculature.