MRI using targeted contrast agents (CA) has emerged as a promising technique to study atherothrombotic disease in vivo. Particularly, the use of targeted Gd and lipid-based nanoparticles has enabled detailed in vivo imaging of various molecular markers of atherosclerotic plaque pathophysiology. For validation purposes, it is crucial that nanoparticle accumulation in the plaque, cellular association and localization can be assessed by ex vivo immuno-histology or fluorescence microscopy of tissue sections. In this review we discuss the various methods that are available for histological evaluation of targeted MRI contrast agents such as lipid-based nanoparticles and iron oxide particles. We discuss the detection of these contrast agents in paraffin-embedded and in cryopreserved tissue sections of atherosclerotic plaques. During the embedding procedure in paraffin, most components of targeted lipid-based nanoparticles are generally washed out, though the actual targeting moieties may be retained in the embedded sections. Therefore staining of the antibody-antigen complex provides a suitable way to visualize the presence of the nanoparticle in the plaque. In cryosections, the localization of nanoparticles can be assessed directly by measuring the fluorescence of an incorporated fluorophore or by secondary stainings of the Gd-containing DTPA lipids or the iron oxide particles. With certain secondary stainings, be it for the contrast agent or for co-localization with the target, the contrast agent itself may interfere with standard histological protocols, yielding false positive results. The here presented techniques enable proper visualization of MR contrast agent accumulation and localization in atherosclerotic plaque, which will provide the validation necessary to advance these lipid-based nanoparticles to the clinic.