Abstract The quantitation of near-trace-element concentrations of calcium (25 ppm atomic fraction) with electron energy loss spectroscopy (EELS) is demonstrated. The data collection, with an energy-stabilized parallel recording spectrometer, subsequent signal processing, and quantitation procedures are described. The quantitative results obtained with EELS, in the biologically relevant range of 1 to 100 mmol/kg, are directly compared with simultaneously collected and previously validated energy-dispersive X-ray spectroscopy (EPMA). The experimentally determined sensitivity of EELS for Ca detection is five-fold better than for EPMA, and the theoretically attainable sensitivity of EELS is ten-fold better than for EPMA. However, the attainment of this sensitivity with EELS is technically more difficult and limited by specimen thickness. The sensitivity of EELS experimentally demonstrated in this study permits the detection of three calcium atoms in a 10 nm diameter spot of an organic matrix, with a field-emission-gun-equipped scanning transmission electron microscope.