Aims: By randomly sampling a known fraction of a pellet of cultured cells, we have accurately estimated the mean number of 50 nm gold nanoparticles accumulated within a single cell. Cellular nanoparticle uptake was measured using a combination of stereological sampling techniques and transmission electron microscopy. Materials & Methods: Nanoparticles were counted individually and their intracellular location was recorded. Quantifying cell and nanoparticle number by analyzing a known fraction of the sample led to precise estimates of intracellular nanoparticle numbers and their spatial locations on an ultrastructural level. We propose a simple and reliable fractionator design and show its applicability and potential using fibroblast cells exposed to 50-nm gold nanoparticles. Results & Conclusion: We demonstrate that this approach is suitable for any electron-dense nanomaterial resolvable by electron microscopy and any convex-shaped cells. In addition, the fractionator concept is flexible enough to be used for spatio-temporal or in vivo studies.