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A method based on flow cytometry was developed which allows measurement of particle size distributions of nanoparticles directly in biological fluids and preparative sorting into distinct size fractions. Fluorescently labelled beads of distinct sizes (0.1–2 μm) were used to establish a correlation between diameter and side scattering intensity (SSC). Simultaneous detection of fluorescence and SSC allowed us to set a threshold on fluorescence thereby providing the possibility to distinguish nanoparticles of interest from other particulate matter (e.g. low density lipoproteins or other serum components) which is frequently present in biological fluids. Finally, a proof of principle was established for sorting a heterogeneous submicron particle population into separate size fractions.