Transmission electron microscopy (TEM) in combination with electron tomography is widely used to obtain nanometer scale three-dimensional (3D) structural information about biological samples. However, studies of whole eukaryotic cells are limited in resolution and/or contrast on account of the effect of chromatic aberration of the TEM objective lens on electrons that have been scattered inelastically in the specimen. As a result, 3D information is usually obtained from sections and not from whole cells. Here, we use chromatic aberration-corrected TEM to record bright-field TEM images of nanoparticles in a whole mount macrophage cell. Tilt series of images are used to generate electron tomograms, which are analyzed to assess the spatial resolution that can be achieved for different vertical positions in the specimen. The uptake of gold nanoparticles coated with low-density lipoprotein (LDL) is studied. The LDL is found to assemble in clusters. The clusters contain nanoparticles taken up on different days, which are joined without mixing their nanoparticle cargo.