The use of nanoparticles for the early detection, cure and imaging of diseases has been proved already to have enormous potentials in different biomedical fields, 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 bio-molecule conjugations. Clearly, the library of nanoparticles generated by combining all possible sizes, shapes and surface physico-chemical 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 multi-scale/multi-physics mathematical models with in-vitro assays and in-vivo intravital microscopy experiments and aims at identifying the optimal combination of size, shape and surface properties that maximize the nanovectors localization within the diseased microvasculature.