Synchrotron radiation phase-contrast computed nanotomography (nano-CT) and two- and three-dimensional (2D and 3D) nanoscopic X-ray fluorescence (nano-XRF) were used to investigate the internal distribution of engineered cobalt nanoparticles (Co NPs) in exposed individuals of the nematode Caenorhabditis elegans. Whole nematodes and selected tissues and organs were 3D-rendered: anatomical 3D renderings with 50 nm voxel size enabled the visualization of spherical nanoparticle aggregates with size up to 200 nm within intact C. elegans. A 20 × 37 nm2 high-brilliance beam was employed to obtain XRF elemental distribution maps of entire nematodes or anatomical details such as embryos, which could be compared with the CT data. These maps showed Co ...