To better study the impact of nanoparticles on both in vitro and in vivo models, tissue distribution and cellular doses need to be described more closely. Here silver nanoparticles were visualized in alveolar macrophages by means of synchrotron radiation micro X-ray fluorescence spectroscopy (SR-μXRF) with high spatial resolution of 3 × 3 μm2. For the spatial allocation of silver signals to cells and tissue structures, additional elemental labeling was carried out by staining with eosin, which binds to protein and can be detected as bromine signal with SR-μXRF. The method was compatible with immunostaining of macrophage antigens. We found that the silver distribution obtained with SR-μXRF was largely congruent with distribution maps from a subsequent laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) of the same tissue sites. The study shows a predominant, though not exclusive uptake of silver into alveolar macrophages in the rat lung, which can be modeled by a similar uptake in cultured alveolar macrophages. Advantages and limitations of the different strategies for measuring nanoparticle uptake at the single cell level are discussed.