Intravital microscopy (IM) for health sciences can be achieved by means of Laser Scanning Microscopy (LSM) in two Photon (2P) excitation conditions using Infrared (IR) illumination which has good penetration in all tissues and organs. Imaging is then performed using 2P emission of fluorescence (2PE) and second harmonic generation (SHG) modes which provide high contrast and good spatial resolution. These modes do reveal the different parts of organs due to differential fluorescence and SHG. In the case of atherotic aorta, for instance, the formation of the atherotic plaque can be visualised and located with respect of aorta's structure: an important application is the diagnosis about unstability or stability of the plaque. Also the spatial resolution of LSM allows revealing the heterogeneous biodistribution of iron oxide core (USPIO) nanoparticles for diagnosis of the atherotic plaque, from the aorta's scale down to the subcellular level: detection of aggregates of USPIOs at the subcellular level supports the model of USPIOs phagocytised by macrophages which target the plaque.